You may also want to consider checking out Affymetrix Powertools. It is a very straightforward piece of software and can generate output that is easily read by R. Paul. On Wed, Apr 17, 2013 at 1:38 PM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > > > On 4/16/2013 8:45 PM, Kalpana G [guest] wrote: >> >> I am a graduate student and new to R and Bioconductor. I have been >> attempting to analyse microarray data from affymetrix rat gene 2.0 ST arrays >> in R. However, I encountered problems that suggest that 2.0 arrays have not >> been updated in Bioconductor (code and error message below). >> >> I wonder if I can overcome this problem by installing the appropriate >> package? If not, please let me know if Bioconductor can currently be used to >> analyse rat 2.0 affymetrix arrays. > > > Yes, but not using the affy package. Instead you want to use either the > oligo or xps package. > > Also, note that mas5 isn't really applicable for the Gene ST arrays > (although I do believe there is some facility to emulate this in xps), as > there are no MM probes. A more reasonable approach would be to use rma. > > Best, > > Jim > > > >> >> Thank you. >> >> -- output of sessionInfo(): >> >>> eset.mas5=mas5(mydata) >> >> background correction: mas >> PM/MM correction : mas >> expression values: mas >> background correcting... >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain RaGene-2_0-st >> Library - package ragene20stcdf not installed >> Bioconductor - ragene20stcdf not available >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr. Paul Geeleher, PhD (Bioinformatics) Section of Hematology-Oncology Department of Medicine The University of Chicago 900 E. 57th St., KCBD, Room 7144 Chicago, IL 60637 -- www.bioinformaticstutorials.com