Transcript SAS® 9.2: Implications for Biotech Bay Area SUG June 7th 2010
SAS
®
9.2 Implications for Biotech
Bay Area SAS User’s Group
June 7
th
2010
Bay Area SUG June 2010
Sarmad Pirzada, MD, MPH Cancer Research & Biostat.
Seattle WA 98199
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Topics for SAS Programmers and IT • 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
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Survival Curves Old Way <9.2
SAS/Stat PHREG Procedures < SAS9.2
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Data Step Lots of SAS Code (>1,200 lines of macro code) SAS Stat Proc Outputs Data Step SAS Graph Programs Output (Not Easily Portable )
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Code Example from < SAS9.1 for Survival Curves
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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;
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SAS/REG Procedures SAS9.2
Other ODS Graphics 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 Bay Area SUG June 2010
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GTL and the SG Procedure
Scatter Plot •Proc Template; ods listing sge= on ;
proc template
; define statgraph classscatter; begingraph ; entrytitle layout 'Weight by Height' overlay; scatterplot ; y=weight x=height; endlayout ; endgraph ; end ;
run
;
proc sgrender run
;
proc sgplot
data data =sashelp.class =sashelp.class; template =classscatter; title 'Weight by Height' ; scatter x =height y =weight;
run
;
Ref: SAS/Stat ® 9.2 User’s Guide: Stat Graphics Using ODS Bay Area SUG June 2010
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GTL and the SG Procedure
Spline Regression Plot ods graphics on ;
proc transreg
data =sashelp.class; model identity (weight)= spline (height); output out =class clm cli p ;
run
;
Ref: SAS/Stat ® 9.2 User’s Guide: Stat Graphics Using ODS Bay Area SUG June 2010
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GTL and the SG Procedure
Box Plot
proc template
; define statgraph classboxplot; begingraph ; entrytitle Distribution' ; 'Gender and Weight layout boxplot overlay; y=weight x=sex; endlayout ; endgraph ; end ;
run
;
proc sgrender run
; data =sashelp.class template =classboxplot;
Ref: SAS/Stat ® 9.2 User’s Guide: Stat Graphics Using ODS Bay Area SUG June 2010
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SAS Graph Template Language (GTL)
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SAS Graph Template Language (GTL)
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SAS/Stat Survival Analysis: PROC PHREG
Macro Errors •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
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SAS/Stat Survival Analysis: Proc PHREG
Hazard Ratios •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
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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!
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IT/Install Related: Most Common ODS Graphics Error
Error Log:
ERROR: The Java proxy is not responding.
ERROR: Unable to load the Java Virtual Machine. Please see the installation instructions or system administrator.
Investigate under Win32/64:
proc options option=appletloc; run; proc options option=jreoptions; run; proc javainfo; run; Bay Area SUG June 2010
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Investigations and e-mails for SAS Tech Support!
Steps for checking JRE Version
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 Files\Java\JRE1.5.0_12\bin\ C:\Program 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: Settings\userid\Application Data\SAS\LOGS C:\Documents and
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IT/Install Related: Most Common ODS Graphics Error
Error Log:
ERROR: The Java proxy is not responding.
ERROR: Unable to load the Java Virtual Machine. Please see the installation instructions or system administrator.
Investigate under Unix/Solaris:
%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.cfg
Add Dsas.app.repository.path=/opt/sas/SAS_9.2/SASVersionedJarRepository/9.2/(machine name) Good SAS Tech Support Contact: Tim Braam SAS Technical Support/Unix Systems Bay Area SUG June 2010
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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/lib32 http://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/9.2
echo '****************************************' > $OUT echo 'starting bin/ODBC_9.2.bash ' >> $OUT echo '****************************************' >> $OUT function move_and_link {while read fn do 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
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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!
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