Dear list,


I would like to use the paCalls from oligo package for filtering probe sets with absence of transcripts. My data are from MoGene-2_0-st and MoEx-1_0-st-v1 array (Affymetrix). My data after reading CEL files is a GeneFeatureSet with 12 samples (6 for control groups, and 6 for experimental groups). What should I do with these data computed by paCalls(PSDABG) as below ?
> library(oligo)
> OligoRawData<-read.celfiles(CEL file lists)
> eset<-rma(OligoRawData)
> dagbPS <- paCalls(OligoRawData, "PSDABG")
What to do next to filter the probe sets? Could you please send me a complete examples and a detailed explanation for it?


In addition, moex10sttranscriptcluster.db can be used for annotation of data from MoEx-1_0-st-v1 array, and both of mogene20stprobeset.db and mogene20sttranscriptcluster.db can be used for that of data from MoGene-2_0-st (including both of gene and lncRNA lists). But only more than half of the probe sets are anotated with gene symbols by below commands.
> results<-decideTests(fit2, method="global", adjust.method="fdr", p.value=0.05, lfc=0.5) #DEGs determination by t tests
> genesymbol = getText(aafSymbol(rownames(results), "moex10sttranscriptcluster.db" ));#annotated by moex10sttranscriptcluster.db for data get from MoEx-1_0-st-v1 array
Only 1217 and 24709 can be annotated by mogene20stprobeset.db and mogene20sttranscriptcluster.db seperately for data of MoGene-2_0-st (length(genesymbol[which(genesymbol!="")])). But the total num is 41345 (length(results)). Only 14966 can be mapped by moex10sttranscriptcluster.db for data of  MoEx-1_0-st-v1 (total num is 23332 - length(results)). Should I need to add some more db for the annotation?


BTW, I am a beginner of this field. I found there are too few documents for examples about how to use functions of oligo package. Could you please also give me some suggestions? Looking forword to your reply. I really appreciate for your any helps. 


Thanks again.


Best regards.


Chao




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