Bay Area SUG June 2010 1 SAS ® 9.2 Implications for Biotech SAS ® 9.2 Implications for Biotech Bay Area SAS User’s Group June 7 th 2010 Sarmad Pirzada,

Bay Area SUG June 2010 1

SASSAS®® 9.2 9.2 Implications for BiotechImplications for Biotech

Bay Area SAS User’s GroupJune 7th 2010

Sarmad Pirzada, MD, MPHCancer Research & Biostat.

Seattle WA [email protected]


• ODS Graphics• SAS Graph Vs. Data

Graphics• Procedures

– PHREG– LIFETEST– SGPLOT– SAS Graph Template– SGPLOT & Related

• A Few Tricks

• SAS Installs• OS Issues

– 32 Vs. 64 Bit– M2 Vs M3– Win Server 2008 R2

• Download Manager• ODBC Driver Issues for

34 Vs. 64 Bit for Unix• JAVA Applet Installs

Topics for SAS Programmers and IT


SAS/Stat PHREG Procedures < SAS9.2

Survival Curves

Old Way <9.2

1. Data Step2. Lots of SAS Code (>1,200 lines of macro code)3. SAS Stat Proc Outputs4. Data Step5. SAS Graph Programs6. Output (Not Easily Portable)


Code Example from < SAS9.1 for Survival Curves


SAS/Stat PHREG Procedures > SAS9.1

Survival Curves

New Way

ods graphics on;proc phreg data=s9321 plots(overlay=stratum)=survival; *ods select survivalplot; model surtim*surind(0)= age ;baseline covariates=ROW out=PRED survival=_all_/ROWID=ISS;run;ods graphics off;quit;


SAS/REG Procedures SAS9.2

Other ODSGraphics

New Way

ods graphics on;proc reg data=sashelp.class; model weight=height; quit;run;ods graphics off;

Ref: SAS/Stat® 9.2 User’s Guide: Stat Graphics Using ODS


GTL and the SG Procedure

Scatter Plot

•Proc Template;ods listing sge=on;proc template;

define statgraph classscatter;begingraph;entrytitle 'Weight by Height';layout overlay;

scatterplot y=weight x=height;

endlayout;endgraph;end;

run;proc sgrender data=sashelp.class template=classscatter;run;proc sgplot data=sashelp.class;

title 'Weight by Height';scatter x=height y=weight;

run;




Spline Regression Plot

ods graphics on;proc transreg data=sashelp.class;

model identity(weight)=spline(height);

output out=class clm cli p;run;




Box Plot

proc template;define statgraph classboxplot;begingraph;entrytitle 'Gender and Weight

Distribution'; layout overlay; boxplot y=weight x=sex; endlayout;endgraph;end;

run;proc sgrender data=sashelp.class template=classboxplot;run;



SAS Graph Template Language (GTL)


SAS Graph Template Language (GTL)


SAS/Stat Survival Analysis: PROC PHREG

•Macros Using PROC PHREG, developed prior to SAS9.2 will run into errors if macros are using default output names

•Usage Note 37170 : Variable name in ParameterEstimates table changed from 'Variable' to 'Parameter'

•Code: Output ParameterEstimate=PE(rename=(Parameter=Variable));

•This Topic covered in usage notes: http://support.sas.com/kb/37/170.html

•In SAS9.2, Plots=Survival (CL), ODS Graphics plot does not extend the survival confidence limits to the last time for censored observations.

•This Topic is covered in usage notes: http://support.sas.com/kb/35/951.html

Macro Errors

http://support.sas.com/kb/37/170.html

http://support.sas.com/kb/35/951.html


SAS/Stat Survival Analysis: Proc PHREG

•GLM Parameterization: Wald Confidence limits provided by the HAZARDRATIO might be incorrect

•Proc PHREG;•Class Gender Group/Param=GLM;

•Model Duration*Censor(1)=Gender X Group X*Group;

•Solution: Need to Compute Custom Hazards Ratios

•HotFix http://ftp.sas.com/techsup/download/hotfix/HF2/A52.html#38391

Hazard Ratios

http://ftp.sas.com/techsup/download/hotfix/HF2/A52.html#38391


SAS/Stat Survival Analysis: Proc PHREG

Other Changes

•Estimation Method: Default method for estimating survival function has changed to Cumulative Hazards from Product Limit (Method=CH Vs. Method=PL). Implication: If default method has been used in the past, the option needs to be changed for reproducing the same results.

•More memory for survival analysis (Usage Notes: 37830)•Where statements may lead to syntax error •Example: Proc Phreg(where(age=1 or age=2) and x=‘B’ data=a; •Fix: Proc Phreg Data=a(where=((age=1 or age=2) and x=‘B’));

•On the Good Side: A Class Option in Phreg!


ERROR: The Java proxy is not responding.ERROR: Unable to load the Java Virtual Machine. Please see the installation instructions or system administrator.

IT/Install Related: Most Common ODS Graphics Error

proc options option=appletloc; run;proc options option=jreoptions; run;proc javainfo; run;

Error Log:

Investigate under Win32/64:


Investigations and e-mails for SAS Tech Support!

1. Check to see if you have this a jvm.dll file here C:\Program Files\Java\JRE1.5.0_12\bin\client\jvm.dll 2. Open a command prompt and go to C:\Program Files\Java\JRE1.5.0_12\bin\ Issue the following at the prompt: java -version Save results for Tech Support: 3. Check your config file: c:\program files\sas\sasfoundation\9.2\nls\en\sasv9.cfg Search for the -jreoptions line

Review every thing that you see on the -jreoptions line 4. Review the logs in the following folder: C:\Documents and Settings\userid\Application Data\SAS\LOGS

Steps for checking JRE Version


ERROR: The Java proxy is not responding.ERROR: Unable to load the Java Virtual Machine. Please see the installation instructions or system administrator.

IT/Install Related: Most Common ODS Graphics Error

%put %sysget(JAVA_HOME) ; %put %sysget(LD_LIBRARY_PATH) ; %put %sysget(LD_LIBRARY_PATH_32) ; %put %sysget(LD_LIBRARY_PATH_64) ; proc javainfo ; run ; proc javainfo picklist 'graph/graph.txt'; run; proc options option=jreptions ; run ;

Modify JREOPTIONS value/opt/sas/SAS_9.2/SASFoundation/9.2/sasv9_local.cfgAdd

-Dsas.app.repository.path=/opt/sas/SAS_9.2/SASVersionedJarRepository/9.2/(machine name)

Good SAS Tech Support Contact: Tim BraamSAS Technical Support/Unix Systems

Error Log:

Investigate under Unix/Solaris:


IT/Install Related DBC Drivers for Oracle 32 Vs. 64 Bit Issues (Notes)

#--- This line assumes that ODBC is located in a directory other than /usr/local #----------------------------------------------------------------------------------------------------------------LD_LIBRARY_PATH=$SYBASE/$SYBASE_OCS/lib:$ODBCHOME/lib/sparcv9:$ODBCHOME/lib:/usr/lib/sparcv9:/usr/lib:$ORACLE_HOME/lib:$ORACLE_HOME/lib32http://support.sas.com/kb/11/728.html oracle 64_____________________________________________#!/bin/bash # IMPORTANT !!! # This script moves 32 bit modules to the executables # so that 32 bit ODBC drivers will work # Must be applied following all Service packs # ---------------------------------------------------#set -x VERS="9_2"OUT="/opt/sas/odbc9.2_change.""`date +'%Y%b%d'`"".log"OUTZIP="/opt/sas/odbc_bkup.""`date +'%Y%b%d%H%M'`"".zip"SASHOME=/opt/sas/SAS_9.2/SASFoundation/9.2echo '****************************************' > $OUTecho 'starting bin/ODBC_9.2.bash ' >> $OUTecho '****************************************' >> $OUTfunction move_and_link{while read fndo echo " " >> $OUT fn2=${fn%_u} echo ". zipping $fn2 to zip file ">> $OUT zip $OUTZIP $fn $fn2 echo ".. moving $fn2 to $fn2.orig64 ">> $OUT mv -i $fn2 $fn2.orig64 echo "... linking $fn to $fn2" >> $OUT ln -s $fn $fn2 echo " " >> $OUT done } cd $SASHOME find $SASHOME -name '*_u' -print >/tmp/sas_odbc_files move_and_link < /tmp/sas_odbc_files rm /tmp/sas_odbc_files


Summary

•SAS9.2 has major changes in its graphics capabilities that are worth changing your code to

•Challenges for IT in terms of 32 Vs. 64 Bit Operating Systems

•Graph Template Language is a Powerful Tool for Programmers

•Portable Graphics

•Check your Essential Macros Prior to Migrating to 9.2M3

•Thank You!