Hi Sean Thanks for your response but I did not get how does it work after I use read.table to read the annotation file in to a data frame For miRNA 2.0 Array annotation file from affymatrix siteFOR my miRna data spleen.affy = ReadAffy() sprma<-rma(spleen.affy) pData(spleen.affy)[,1]<-c("N","N","N","P","P","P","P","P","P","N","N", "N") exprs(sprma) here I want to apply annotation file read in data frame to my data how to go about it thanks -- output of sessionInfo(): > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Ireland.1252 LC_CTYPE=English_Ireland.1252 [3] LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C [5] LC_TIME=English_Ireland.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mirna20cdf_2.8.0 affy_1.30.0 Biobase_2.12.2 loaded via a namespace (and not attached): [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.1 > -- Sent via the guest posting facility at bioconductor.org.

Hi, Attia. I'm guessing that you want to put your data into the featureData slot. You might take a look at the Biobase vignette about ExpressionSets and also the fData() method. Sean On Fri, Oct 21, 2011 at 8:10 AM, Attia [guest] <guest at="" bioconductor.org=""> wrote: > > Hi Sean > Thanks for your response but ?I did not get how does it work ?after I use read.table to read the annotation file in to a data frame > For miRNA 2.0 Array ?annotation file ?from affymatrix siteFOR my miRna data > spleen.affy = ReadAffy() > sprma<-rma(spleen.affy) > pData(spleen.affy)[,1]<-c("N","N","N","P","P","P","P","P","P","N","N ","N") > > exprs(sprma) > here I want to apply annotation file read in data frame > to ?my data how to go about it > thanks > > ?-- output of sessionInfo(): > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_Ireland.1252 ?LC_CTYPE=English_Ireland.1252 > [3] LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C > [5] LC_TIME=English_Ireland.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] mirna20cdf_2.8.0 affy_1.30.0 ? ? ?Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 ? ? ? ? preprocessCore_1.14.0 tools_2.13.1 >> > > > -- > 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 >