SAS healthcare workshop 18 nov 2011
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Transcript of SAS healthcare workshop 18 nov 2011
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Healthcare Workshop 201118 November 2011
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Healthcare Workshop 2011
Agenda
2.00 - 4.00pm : Statistical Analysis in Healthcare Industry showcasing SAS Enterprise Guide and SAS STAT capabilities in HealthCare analytics - Giuseppe Manai , SAS Senior Pre-sales Consultant- Jun Yao, SAS Pre-sales Consultant
4.00 - 4.15pm : Tea Break
4.15 - 5.15pm : Powerful Features of SAS: Reporting and Presenting Relevant Statistical Summary of Clinical Data - Dr Pryseley N. Assam, Adjunct Assistant Professor for Centre for Quantitative Medicine, Duke-NUS Graduate Medical School & Biostatistician at Singapore Clinical Research Institute
5.15 - 5.45pm : Application of PROC Frequency in Clinical Analysis - Mr Gabriel Jiang, Senior Statistician-Computation, Lilly-NUS Centre for Clinical Pharmacology Pte. Ltd.
5.45 - 6.00pm : Q&A and Closing
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Copyright © 2011, SAS Institute Inc. All rights reserved.Copyright © 2011, SAS Institute Inc. All rights reserved.
Statistical Analysis inHealthcare IndustryGiuseppe Manai, SAS Senior Pre-sales Consultant
Jun Yao, SAS Pre-sales Consultant
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Healthcare Workshop 2011
Outline
SAS Business Analytics Framework Giuseppe
Introduction to SAS Enterprise Guide SAS Enterprise Guide Workspace
Tasks and Wizards: Easy in Enterprise Guide
Examples + Hands-on Activity
Statistical techniques
Scheduling Jun Yao
What’s New in SAS Enterprise Guide 5.1
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Healthcare Workshop 2011
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SAS Healthcare Workshop 2011
How do we do it?
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SAS Healthcare Workshop 2011
BUSINESS SOLUTIONS
How do we do it?
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SAS Healthcare Workshop 2011
INFORMATION MANAGEMENT
BUSINESS SOLUTIONS
How do we do it?
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SAS Healthcare Workshop 2011
BUSINESS SOLUTIONS INFORMATION MANAGEMENT
ANALYTICS
How do we do it?
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SAS Healthcare Workshop 2011
REPORTING
BUSINESS SOLUTIONS INFORMATION MANAGEMENT ANALYTICS
How do we do it?
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SAS Healthcare Workshop 2011
Healthcare Providers Using SAS
Business IssuesFacing problem in data integration and data analysis. Different software was being used in each department making consolidation of the data difficult to achieve or even visualise.
SolutionIntegration of the clinical and medical management data analysis.
ResultsPatient response times are much quicker and effective.
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SAS Healthcare Workshop 2011
Healthcare Providers Using SAS
Business Issues Large data analysis was slow and difficult. Separate software was being used in different departments causing problems with data integration and resulting in analytical limitations.
SolutionIntegrates the different departments under a single repository of information enabling access to all in a standardised single version of the truth.
Results standardized records and reports
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SAS Healthcare Workshop 2011
Introduction to SAS Enterprise Guide
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SAS Healthcare Workshop 2011
Introduction to Enterprise Guide
Quick access and manipulation of data
Carry out basic and complex analysis
Easy to use basic reporting
Easy to use Quick
Intuitive
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SAS Healthcare Workshop 2011
Introduction to Enterprise Guide
What does SAS EG do? Point-and-click GUI
Menu- and wizard- driven
Enables fast data analysis and results publishing
Fast-track learning data analysis
Generates code in background for productivity
Deploys analyses and forecasts in real time.
Who is SAS EG designed for? Business analysts with no SAS programming experience
SAS programmers
Statisticians
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Healthcare Workshop 2011
Introduction to SAS Enterprise GuidePoint-and-click interface for managing data and generating reports.
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SAS Healthcare Workshop 2011
Introduction to SAS Enterprise Guide
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SAS Healthcare Workshop 2011
Introduction to Enterprise GuideProgramming Interface
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SAS Healthcare Workshop 2011
SAS Enterprise Guide Interface
Data sources
SAS programs and logs
Tasks and Queries
Results
Informational Notes for Documentation
You can control contents, sequencing, and updating of a project.
A PROJECT is a single file that serves as a collection of:
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Healthcare Workshop 2011
SAS Enterprise Guide Interface
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SAS Healthcare Workshop 2011
Behind the ScenesAs you build tasks, Enterprise Guide generates SAS code.
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SAS Healthcare Workshop 2011
Tasks and Wizards: Easy in EG
Data Management Quickly Visualize, Open or Import Data
Join Datasets efficiently
Create Frequency Reports
Program Editor
Visualization Graphs (Histogram/ Bar-Chart/Pie Chart)
Statistical techniques t-test
ANOVA
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SAS Healthcare Workshop 2011
Examples
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SAS Healthcare Workshop 2011
Building a SAS Enterprise Guide Project
1. Add Datasets (can also import from Excel)
2. Perform a task
3. One-way frequencies and statistical tests
4. Automate a Process
5. Graphing
6. Create Reports (List Data)
7. Summary Statistics
8. Simple Linear Regression
9. t-Test and ANOVA
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SAS Healthcare Workshop 2011
Common Data Formats
SAS datasets
Microsoft Excel and Access
DBMS tables
Text files
JMP
HTML
SPSS
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SAS Healthcare Workshop 2011
One-Way Frequency Report
The One-Way Frequencies task can be used to generate: Frequency counts Percentages Graphs Statistical tests to analyze the distribution of your data
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SAS Healthcare Workshop 2011
Types of Graphs
The Graph menu
includes all of the
advanced graph tasks
as well as the wizards.
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SAS Healthcare Workshop 2011
Graphs Using SAS Enterprise Guide
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SAS Healthcare Workshop 2011
Characterize Data
The Characterize Data task is an exploratory
task that produces automatically statistics and
graphs for all variables, grouping by type of
variable (i.e. categorical, interval, etc.)
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SAS Healthcare Workshop 2011
Summary Statistics Report
Calculate summary statistics based on groups within the data.
Can produce reports, graphs and data sets as output.
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SAS Healthcare Workshop 2011
Automate a Process
To automate a process flow you simply name it
Autoexec
This will run the process flow when opening the project
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SAS Healthcare Workshop 2011
Hands-on activity (10-15 min)
Try to: Import a dataset
Create a task
Graph the results
Automate the process
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SAS Healthcare Workshop 2011
Simple Linear Regression Analysis
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SAS Healthcare Workshop 2011
Simple Linear Regression Analysis
The objectives of simple linear regression are to:
Assess the significance of the predictor variable
in explaining the variability or behavior of the response
variable
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SAS Healthcare Workshop 2011
Simple Linear Regression Model
b0
1 unit
b1 units
b 0 + b 1
X
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SAS Healthcare Workshop 2011
Simple Linear Regression Model
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SAS Healthcare Workshop 2011
Performing Simple Linear Regression
Example ……
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SAS Healthcare Workshop 2011
t-Test and ANOVA
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SAS Healthcare Workshop 2011
Performing t-Test (Paired Sample)
Analyze differences between two population means using the t-Test task.
Perform a paired-sample t-test to determine
whether a medication was successful in reducing
blood pressure.
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SAS Healthcare Workshop 2011
Scenario 1
DatasetTo observe the effectiveness of a medication in reducing blood pressure, an experiment was conducted in which researchers collected data from a random sample of individuals who were considered to have high blood pressure. The diastolic blood pressure of these individuals was recorded, after which they were placed on the medication. One month later, their diastolic pressure was recorded again.
ObjectiveDetermine if the data gives good evidence that the medication was effective in reducing blood pressure by carrying out a test of significance (at level α = 0.05), pairing the two blood pressure recordings for each subject.
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SAS Healthcare Workshop 2011
Performing Simple Linear Regression
Example ……
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SAS Healthcare Workshop 2011
Analysis of Variance (One-Way ANOVA)
Perform a one-way ANOVA to determine whether
there are significant differences between four drugs
in mean increase in systolic blood pressure.
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SAS Healthcare Workshop 2011
Scenario 2
DatasetConsider a pharmaceutical company that has recently focused on the effect of its potential products on blood pressure. Researchers conducted a study in which the subjects were 72 individuals with one of three diseases. Eighteen individuals were randomly assigned to each of the four drugs. The treatments were administered over time and the increase in systolic blood pressure was recorded.
ObjectiveDetermine whether there are significant differences between the mean increases in systolic blood pressure for the four drugs. If there are, evaluate which drugs differ and how greatly they differ.
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SAS Healthcare Workshop 2011
One-Way ANOVA
Example…….
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SAS Healthcare Workshop 2011
Hands-on activity (10-15 min)
Explore Enterprise Guide’s tasks
Use data sets provided
Modify variables
Use different tasks
Create graphs and reports
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SAS Healthcare Workshop 2011
Task Scheduling via Enterprise Guide
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What’s New in SAS Enterprise Guide 4.3
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SAS Healthcare Workshop 2011
SAS® Enterprise Guide 4.3
Release Objectives User productivity Integration Performance
Key Features New program editor with auto complete and integrated syntax help Enhanced OLAP Analysis capabilities for enriched user experience Tighter integration with SAS WRS Reports and JMP Rapid Predictive Modeling (RPM) Enterprise Miner integration New performance enhancement capabilities with Explicit SQL pass-
through option, In-database optimized syntax generation and Integration for Grid enablement
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SAS Healthcare Workshop 2011
Enhancements for SAS Programmers
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SAS Healthcare Workshop 2011
Enhanced Program Editor
Mouse over Tooltip with details for SAS PROCS, SAS Functions
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SAS Healthcare Workshop 2011
Enhanced Program Editor - Autocomplete
Connects to data library listing accessible data tables
Provides list of SAS PROCS, SAS Functions and Macro variables, assisting user while coding
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SAS Healthcare Workshop 2011
Enhanced Program Editor
Converts code into Indented Format
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SAS Healthcare Workshop 2011
Enhanced Program Editor – Analyze Program
Coverts lines of Code into Process Flow for visual representation and ease understanding of the program flow
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SAS Healthcare Workshop 2011
Adhoc Analysis Enhancements
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SAS Healthcare Workshop 2011
OLAP Analyzer – Enhanced Filtering options
Enhanced filter options with Example support
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SAS Healthcare Workshop 2011
OLAP Analyzer - Enhanced MDX Editor
• Drag-n-Drop support to add measures/dimensions to the MDX
• Show Line numbers for MDX
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SAS Healthcare Workshop 2011
OLAP Analyzer - Enhanced MDX Editor
New options for Search
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OLAP Analyzer - New Chart Types
New Chart Types• Scatter Plot• Tile Chart
• Automatic Charting (creates a chart based on Dimensions and Measures selected in crosstab)
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SAS Healthcare Workshop 2011
OLAP Analyzer – Enhanced Explorer View
Apply Path to Siblings option for a smoother data exploration
experience.
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SAS Healthcare Workshop 2011
Integration with JMPData opened in EG 4.3
Data opened in JMP
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Integration with Rapid Predictive Modeler
Self service analysis and report generation using wizard driven RPM task
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What’s New in SAS Enterprise Guide 5.1
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SAS Healthcare Workshop 2011
SAS® Enterprise Guide 5.1
Release Objectives Leverage the capabilities of SAS 9.3 platform Enriched User Experience Increased productivity
Key Features Enhanced program editor with auto complete for dataset
variables Improved tooltip support for SAS keywords with help
documents Enhanced OLAP Analysis capabilities for enriched user
experience Reusable queries (Query Templates and Sub Queries) Enriched interface for creating Stored Process
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SAS Healthcare Workshop 2011
Enhanced Program EditorEnriched user experience and increased productivity
Provides the ability to view the list of variables from the selected data set.
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SAS Healthcare Workshop 2011
Enhanced Program EditorEnriched user experience and increased productivity
Enhanced tool tip support with web link to Product Documentation and Samples.
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SAS Healthcare Workshop 2011
Enhanced Program EditorEnriched user experience and increased productivity
Ability to split and stack the programming window – side by side or tiled
• Work with different parts of same program in single view
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SAS Healthcare Workshop 2011
Adhoc OLAP AnalysisEnriched user experience
Predefined Calculation Functions for time-series data analysis
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SAS Healthcare Workshop 2011
Adhoc OLAP AnalysisEnriched user experience
Refined Contextual Menu for defining Totals and % of Totals
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SAS Healthcare Workshop 2011
Reusable Queries
1 Define queries and save them as Templates
2 Use existing queries as Sub-Queries to filter data
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SAS Healthcare Workshop 2011
Options for Code Submissions
Ability to define the Code Submission options and gain
increased performance in a grid enabled environment
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SAS Healthcare Workshop 2011
Any Questions?
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SAS Healthcare Workshop 2011
Tea-Break
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Copyright © 2011, SAS Institute Inc. All rights reserved.Copyright © 2011, SAS Institute Inc. All rights reserved.
Powerful SAS Features: Reporting & Presenting Statistical Summary of Clinical DataPryseley Assam (PhD)Biostatistician, Singapore Clinical Research InstituteAssistant Professor, Duke-NUS Graduate Medical School
SAS Healthcare Workshop
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SAS Healthcare Workshop 2011
Outline
Introduction
A case study – retrospective study
Some useful SAS features (summaries, reports)
Remarks
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SAS Healthcare Workshop 2011
Introduction
Mandatory Clinical Trial Registration
» The International Committee of Medical Journal Editors
» Pharmaceutical Research & Manufacturers of America
New England Journal of Medicine (Sept 16 issue 2004)
… patients have a right to trust that investigators will not
only minimize risks to the participants but also will
conduct research ethically and report it completely and
honestly.
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SAS Healthcare Workshop 2011
Introduction
Obligation to report/publish research findings
» Participants (patients)
» Scientific committee
» Sponsors
Guidelines for reporting
» Randomized controlled trials: CONSORT
» Systematic reviews and meta-analysis: PRISMA
» Observations studies: STROBE
» Diagnostic studies: STARD
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SAS Healthcare Workshop 2011
Introduction
Complete and honest reporting is facilitated by appropriate study design, conduct and analysis, in accordance with the study objectives
Increasing demand for statistical input in
healthcare studies
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SAS Healthcare Workshop 2011
Introduction
Statistical report
» Design, size, and outcomes of the study
» Patient selection flow chart
» Summary statistics
» Graphs
» Analysis
Automated summaries and report attributes
Statistical data review
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SAS Healthcare Workshop 2011
Case Study - DUMIN
Motivation
» RCTs are not representative of practice
» Strict measurement based-care approach
» Higher doses than found in typical clinical care
Data description
» All outpatients with clinical depression (and anxiety)
» On one antidepressant medication for at least 1week
» At least two assessment within the 9 weeks of treatment
» Study period: January 2000 to December 2010
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SAS Healthcare Workshop 2011
Case Study - DUMIN
Objectives
Describe overall response rates
» CGI-I
» CGI-S change from baseline
Is outcome related to
» Baseline severity
» Duration of treatment
Identify clinical features associated with outcomes
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Some useful SAS Features
Summarizing Data
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SAS Healthcare Workshop 2011
Summarizing Data
Listings
» Useful for providing detail reports; a detail report gives you at least one row of information in your report for selected observations (patients/events) in the data set.
» Reporting severe adverse events in RCT
» DATA Steps, PROC TRANSPOSE, PROC SQL
» PROC PRINT, PROC REPORT
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SAS Healthcare Workshop 2011
Summarizing Data
Listings
Enhancements
» Labels of variables (DATA steps, PROC SQL)
» Formats for values of variables (PROC FORMAT)
» Styles and templates
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SAS Healthcare Workshop 2011
Summarizing Data
Listings
» Suicidal patients – PROC PRINT (WHERE clause)
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SAS Healthcare Workshop 2011
Summarizing Data
Listings
PROC FORMAT;VALUE $ SexF "M" = "Male"
"F" = "Female";
RUN;
PROC PRINT DATA=LOC.Dumin (FIRSTOBS=1 OBS=25) NOOBS LABEL BLANKLINE=5 N;
FORMAT Gender $SexF.;WHERE Suicide = "Yes";VAR BackgroundID Gender Race2 Age_Bin Diagnosed
Suicide Mono Med_Class Substance Subst;
RUN;
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SAS Healthcare Workshop 2011
Summarizing Data
Listings
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SAS Healthcare Workshop 2011
Summarizing Data
Listings
» Suicidal patients with ≥ 2 assessments – PROC SQL
PROC SQL;CREATE TABLE Suic_2 ASSELECT DISTINCT BackgroundID, Gender, Race2, Age_Bin,
Diagnosed, Suicide, Mono, Med_Class, Substance, Subst, Suicide
FROM LOC.DuminWHERE BackgroundID IN
(SELECT DISTINCT BackgroundID FROM LOC.Visits GROUP BY BackgroundID HAVING COUNT(ENum) > 2 )
;QUIT;
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SAS Healthcare Workshop 2011
Summarizing Data
Listings
» Suicidal patients with ≥ 2 assessments – PROC SQL
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SAS Healthcare Workshop 2011
Summarizing Data
Listings
» Safety analysis in RCTs
ID/Grp
First dose date/Last dose
date
VisitNo.
Onset date/Resolution
dateSystem Organ Class
Preferred
Term
Investigator
Term
Relationto study
drug
Trt givento AE
1356 / A 02JUL2011 / 12AUG2011 V2 01JUL2011 /
01JUL2011 Nervous system disorders Dizziness GIDDINESS FOR 3 HOURS Unknown No
1356 / A02JUL2011 / 12AUG2011 V2 01JUL2011 /
05JUL2011 Psychiatric disorders Somnolence DAY-TIME DROWSINESS Unknown No
1356 / A02JUL2011 / 12AUG2011 V6 30JUL2011 /
03AUG2011 Psychiatric disorders Somnolence DAY-TIME DROWSINESS Likely No
1463 / B 23SEP2011 / 16NOV2011 V3 07OCT2011 /
07OCT2011
General disorders and administration site conditions
Feeling hot WARM SENSATION Not related No
1463 / B23SEP2011 / 16NOV2011 V4 19OCT2011 / . Musculoskeletal and
connective tissue disorders Arthralgia LEFT ANKLE PAIN Not related No
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SAS Healthcare Workshop 2011
Summarizing Data
Summary report
» A summary report generally does some form of collapsing of observations so that each row in the report represents information from more than one observation
» Demographic and baseline clinical characteristics
» Efficacy and safety outcomes
» PROC SQL, MEANS, SUMMARY, FREQ, UNIVARIATE
» PROC TABULATE, REPORT, TRANSPOSE
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SAS Healthcare Workshop 2011
Basic Summary
Outcomes – PROC MEANS
PROC MEANS DATA=LOC.Dumin MISSING N NMISS MEAN STD MIN MAXNONOBS MAXDEC=3;
CLASS Suicide;VAR CGI_Entry CGI_1 CGI_2;
RUN;
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SAS Healthcare Workshop 2011
Basic Summary
Demographics – PROC FREQ
PROC FREQ DATA=LOC.Dumin; TABLE Gender Age_Bin
Race2 Diagnosed ;RUN;
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SAS Healthcare Workshop 2011
Basic Summary
Demographics – PROC FREQ
PROC FREQ DATA=LOC.Dumin; TABLE Gender Age_Bin Race2 Diagnosed / MISSING ;RUN;
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SAS Healthcare Workshop 2011
Basic Summary
Demographics – PROC FREQ
PROC FREQ DATA=LOC.Dumin ORDER=INTERNAL; TABLE CGI_1 / MISSING OUT=CGI OUTCUM;
TABLE Suicide*CGI_1 / MISSING OUT=CGIS OUTPCT;
TABLE Diagnosed*CGI_2 / MISSING OUT=CGIS OUTPCT;
RUN;
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SAS Healthcare Workshop 2011
Summary Tables
PROC TABULATE
» Very useful descriptive statistics
» Simple but powerful methods to create tabular reports
» Establishing hierarchical relationships between the variables
» Mechanisms for labeling and formatting variables and procedure- generated statistics.
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SAS Healthcare Workshop 2011
Summary Tables
Tables of summary statistics - TABULATE
PROC TABULATE DATA=LOC.Dumin ORDER=FREQ;
CLASS Gender Age_Bin Subst Race2 Med_Class Mono
;VAR CGI_1;TABLE ALL="All Patients"
Gender Age_Bin Med_Class*Mono Subst Race2, ALL="All Patients"*(N REPPCTN="%") CGI_1*(MEAN STD LCLM UCLM);
RUN;
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SAS Healthcare Workshop 2011
Summary Tables
Continuous outcome - TABULATE
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SAS Healthcare Workshop 2011
Summary Tables
Continuous outcome - TABULATE
DATA LOC.Dumin;SET LOC.Dumin;Sex = "Gender";Races = "Race";AgeGrp = "Age Groups";SuicP = "Suicidality";
RUN;
PROC TABULATE DATA=LOC.Dumin MISSING ORDER=FREQ;FORMAT Suicide $Sui.;
CLASS Gender Age_Bin Race2 Suicide Sex Races AgeGrp SuicP ;
VAR CGI_1;TABLE ALL="All Patients"
Sex*Gender AgeGrp*Age_Bin Races*Race2 SuicP*Suicide , ALL="All Patients"*(N REPPCTN="%")
CGI_1*(MEAN STD LCLM UCLM) /RTS=25 INDENT=4 ;RUN;
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SAS Healthcare Workshop 2011
Summary Tables
Continuous outcome - TABULATE
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SAS Healthcare Workshop 2011
Summary Tables
Binary outcome - TABULATE
PROC FORMAT;VALUE CGIIB 1 - 3 = "Improvement"
4 - 7 = "No Improvement"Other = " "
;RUN;
PROC TABULATE DATA=LOC.Dumin MISSING ORDER=FREQ;FORMAT CGI_1 CGIIB.;CLASS CGI_1 Gender Race2 Age_Bin Subst
Sex Races AgeGrp ASubs;TABLE ALL="All Patients"
Sex*Gender AgeGrp*Age_Bin Races*Race2 ASubs*Subst, ALL="All Patients"*(N REPPCTN="%") CGI_1*(N REPPCTN="%") /RTS=25 INDENT=4 ;
RUN;
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SAS Healthcare Workshop 2011
Summary Tables
Cell Percentages - TABULATE
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SAS Healthcare Workshop 2011
Summary Tables
Row Percentages - TABULATE
» Useful for comparison
PROC TABULATE DATA=LOC.Dumin MISSING ORDER=FREQ;FORMAT CGI_1 CGIIB.;CLASS CGI_1 Gender Race2 Age_Bin Subst
Sex Races AgeGrp ASubs;TABLE ALL="All Patients"
Sex*Gender AgeGrp*Age_Bin Races*Race2 ASubs*Subst, ALL="All Patients"*(N REPPCTN="%") CGI_1*(N ROWPCTN="%") /RTS=25 INDENT=4 ;
RUN;
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SAS Healthcare Workshop 2011
Summary Tables
Row Percentages - TABULATE
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SAS Healthcare Workshop 2011
Summary Tables
Proportions of Covariates - TABULATE
Direct cost
What are the respective contributions of the components
of direct cost and the type of cases to the total direct cost?
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SAS Healthcare Workshop 2011
Summary Tables
Proportions of Covariates - TABULATE
PROC TABULATE DATA=LOC.H_Expend FORMAT=8.2; WHERE Cost = "Direct"; CLASS CT Cost CC; VAR Value; TABLE CC* (Sum='Cost per Case' PCTSUM<CC>='% by Direct Cost' PCTSUM<CT>='% by Case Type' PCTSUM='Overall %') , Value*CT /RTS=35 INDENT=4;RUN;
PROC TRANSPOSE
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SAS Healthcare Workshop 2011
Summary Tables
Proportions of Covariates - TABULATE
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SAS Healthcare Workshop 2011
Saving Outputs
ODS RTF (Rich text format)
» Editable reports (manuscripts)
ODS PDF
» Non-editable reports
» Validation results, Safety and protocol deviations
ODS HTML
» Websites
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SAS Healthcare Workshop 2011
Saving Outputs
BasicsX “CD C:\SAS HealthCare Workshop\Figures”;
ODS RTF File=“File Name.rtf";
SAS PROCEDURES
ODS RTF CLOSE;
OPTIONS ORIENTATION=LANDSCAPEODS RTF File=“File Name.rtf“ STYLE=myStyle; TITLE ; TITLE2 ; ODS TEXT=“Include Text”;
SAS PROCEDURES
ODS RTF CLOSE;
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SAS Healthcare Workshop 2011
Outputs for Reports
Stored RFT Files (Templates)
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SAS Healthcare Workshop 2011
Outputs for Reports
Style = Journal
+ FORMAT
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SAS Healthcare Workshop 2011
Summary Reports
Employing multiple procedures, styles and format
» PROC MEANS, UNIVARIATE, FREQ, …
» PROC TABULATE, PROC REPORT
» ODS RTF
» OPTIONS Statement
» MACROS
» …
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SAS Healthcare Workshop 2011
Automated Summary Reports
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SAS Healthcare Workshop 2011
Automated Summary Reports
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Copyright © 2011, SAS Institute Inc. All rights reserved.Copyright © 2011, SAS Institute Inc. All rights reserved.
Some useful SAS Features
Depicting Data
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SAS Healthcare Workshop 2011
Depicting Data
SAS GRAPH - Procedures
» SGPLOT, SGPANEL, SGSCATTER, …
» GREPLAY
ODS Graphics (over 60 procedures)
» SAS/Base
» SAS/STAT, SAS/ETS, SAS/QC
Graphical representations of data are often more
easily understood and remembered than tabular
forms
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SAS Healthcare Workshop 2011
Depicting Data
ODS Graphics ONProcedure optionsDefault plot createdPLOTS=syntax [non-default plots]
ODS Graphics OFF
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SAS Healthcare Workshop 2011
Depicting Results
Regression diagnostics - Example
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SAS Healthcare Workshop 2011
Depicting Data
Basic things to note for ODS Graphics
Formats (IMAGEFMT=)
» PNG, PS, TIFF
» JPEG, GIF, PDF, WMF
X "CD C:\SAS HealthCare Workshop\Figures";
ODS GRAPHICS ON / IMAGENAME="MyFigure" IMAGEFMT=;
GRAPH/STAT PROCEDURE DATA= ;PROCEDURE OPTIONS
RUN;
ODS GRAPHICS OFF;
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SAS Healthcare Workshop 2011
Depicting Data - DUMIN
Patient selection
18475 patients
1722 (9%) Eligible patients
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SAS Healthcare Workshop 2011
Depicting Data - DUMIN
Primary outcome (CGI-I)
» INSET and FORMAT statements
Requested plotFinal plot
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SAS Healthcare Workshop 2011
Primary outcome (CGI-I)
Depicting Data - DUMIN
SGPANEL
PROC FREQ + SGPANEL
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SAS Healthcare Workshop 2011
Primary outcome (CGI-I)
Depicting Data - DUMIN
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Depicting Data
Multiple graphs in a figure
» PROC GREPLAY
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CGI outcomes
» IMAGEFMT=PS and LaTeX
Depicting Data - DUMIN
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Absolute and cumulative percentages
Depicting Data
FREQ+
SGPLOT
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SAS Healthcare Workshop 2011
Remarks
Reporting results of clinical studies is mandatory
Results need to be represented concisely and precisely
SAS provides extensive tools for summarizing data and preparing results for reporting, especially when used in conjunction with other software
» Use the SAS thoughtfully
Having the right tools is important!
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Any Questions?
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Application of PROC Frequency in Clinical AnalysisGabriel Jiang Senior Statistician-Computation, Lilly-NUS Centre for Clinical Pharmacology Pte. Ltd.
SAS Healthcare Workshop 2011
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PROC FREQ
What else can we do other than counting observations and putting them in cross tabulation or n x n ways?
Common syntaxPROC FREQ <options> ;
BY variables ;
EXACT statistic-options </ computation-options> ;
OUTPUT <OUT=SAS-data-set> options ;
TABLES requests </ options> ;
TEST options ;
WEIGHT variable </ option> ;
run;
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PROC FREQ
Agenda
- Filling in zeroes with Sparse Option
- Complement with ODS Graphics
- Controlling displayed output
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PROC FREQ (1)
Scenario: I need to have lots of ‘0’ values in my tables, to show that there were no event occurrences
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ExampleLots of zeroes
PROC FREQ (1)
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PROC FREQ
Solution?
You can create zeroes in a dummy dataset, and proceed to merge with the original ‘incomplete’ dataset
Another question:
It’s troublesome to create the dummy dataset, I don’t even know which combinations are missing
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PROC FREQ
Solution:
If you are using PROC FREQ, then there is an easy solution
Use the SPARSE Option!
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PROC FREQ
Sample code
Original code:
proc freq data=heart1;
table sex*chol_status*weight_status/ out=all noprint;
run;
New addition:
proc freq data=heart1;
table sex*chol_status*weight_status/ out=all sparse noprint;
run;
#Using data from SASHELP.HEART
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PROC FREQ
Observations with missing Cholesterol Status
Previously missing combinations of Sex, Cholesterol Status and
Weight Status
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PROC FREQ
Missing zero
Combinations incomplete
Output without the Sparse option
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PROC FREQ
Cholesterol Status is missing
Previously, combination of categories that
were not available
Final Output
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PROC FREQ (2)
Scenario: I don’t want to have to write a whole set of GPLOT statements to get plots from PROC FREQ outputs, what should I do?
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PROC FREQ
SAS/Graph? Maybe by using PROC GPLOT?
PROC GPLOT <DATA=input-data-set> <ANNOTATE=Annotate-data-set> <GOUT=<libref.>output-catalog> <IMAGEMAP=output-data-set > <UNIFORM>;
BUBBLE plot-request(s) </option(s)>;
BUBBLE2 plot-request(s) </option(s)>;
PLOT plot-request(s) </option(s)>;
PLOT2 plot-request(s) </option(s)>;
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Combining with ODS Graphics
ODS GRAPHICS ON;
PROC FREQ <options> ;
BY variables ;
EXACT statistic-options </ computation-options> ;
OUTPUT <OUT=SAS-data-set> options ;
TABLES requests / PLOTS < ( global-plot-options ) > < = plot-request < ( plot-options ) > > ;
TEST options ;
WEIGHT variable </ option> ;
run;
ODS GRAPHICS OFF;
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Combining with ODS Graphics
Plots
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PROC FREQ
Sample Code
ods graphics on;
proc freq data=heart;
table sex*chol_status*weight_status/ plots(only)=freqplot;
run;
ods graphics off;
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PROC FREQ
Sample Output
table sex*chol_status*weight_status/ plots(only)=freqplot(orient=vertical);
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PROC FREQ
Sample Output
table sex*chol_status*weight_status/ plots(only)=freqplot(orient=horizontal);
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table sex*chol_status*weight_status/ plots(only)=freqplot(orient=horizontal scale=freq|log|percent|sqrt type=barchart);
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PROC FREQ
table sex*chol_status*weight_status/ plots(only)=freqplot(orient=vertical scale=freq type=dotplot);
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PROC FREQ
table sex/ plots(only)=cumfreqplot(orient=horizontal scale=freq);
table sex/ chisq plots(only)=deviationplot(orient=horizontal);
Cumulative Frequency Plot Deviation Plot
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Frequency plots for multi-way tables
plots(only)=freqplot(orient=horizontal twoway=groupvertical); plots(only)=freqplot(orient=horizontal twoway=grouphorizontal);
plots(only)=freqplot(orient=horizontal twoway=stacked type=dotplot);plots(only)=freqplot(orient=horizontal twoway=stacked type=barchart);
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Kappa plots
plots(only)=kappaplot (npanelpos=0);c plots(only)=kappaplot (npanelpos=0 stats);
plots(only)=kappaplot (npanelpos=1);
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Kappa plots
plots(only)=kappaplot(npanelpos=0 order=descending stats); plots(only)=kappaplot(npanelpos=0 order=ascending stats);
plots(only)=kappaplot(npanelpos=0 order=ascending stats range=clip); plots(only)=kappaplot(npanelpos=0 order=ascending stats range=(-0.1,0.0));
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PROC FREQ
Kappa plot Weighted Kappa plot
plots(only)=kappaplot(npanelpos=0); plots(only)=wtkappaplot(npanelpos=0);
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Odds Ratio Plot
plots(only)=oddsratioplot(npanelpos=0 stats); plots(only)=oddsratioplot(npanelpos=0 logbase=10 stats);
plots(only)=oddsratioplot(npanelpos=0 logbase=2 stats); plots(only)=oddsratioplot(npanelpos=0 logbase=e stats);
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PROC FREQ (3)
Scenario: I have generated some outputs using PROC FREQ… how can I change the format of the values?
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PROC FREQ
Using the FORMAT= option
Note: The FORMAT= option applies only to cross-tabulation tables displayed in the default format. It does not apply to cross-tabulation tables produced with the LIST or CROSSLIST option.
For one way tables, you have to use PROC TEMPLATE
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PROC FREQ
Default (BEST6./BEST7.)
proc freq data=heart;
table sex*chol_status*weight_status / nopercent norow nocol ;
run;
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PROC FREQ
Using Format= option
proc freq data=heart;
table sex*chol_status*weight_status / nopercent norow nocol format=12.3;
run;
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PROC FREQ
Question: If I want the layout as a list?
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PROC FREQ
Using LIST option
proc freq data=heart;
table sex*chol_status*weight_status / nopercent norow nocol list;
run;
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References
Base SAS® 9.2 Procedures Guide Statistical Procedures 3rd Edition
http://bit.ly/bcT6Yt
SAS 9.2 Online Documentation
http://support.sas.com/documentation/cdl_main/index.html
Chris Moriak (2002) , The Sparse Option in PROC FREQ: Little Known, Yet Powerful, NESUG15
Mike Rhoads (2009), Changing the Numeric Format of PROC FREQ Output
http://support.sas.com/kb/24/822.html
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Any Questions?
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SAS Healthcare Workshop 2011
Thank you for your participation in SAS Healthcare Workshop
2011!
Have A Great Day!
If you have any further questions, you may email to
Valeria Tan, Account Manager for Healthcare Sector at [email protected]
Customer Success Team at [email protected]