Hello Mike,

I tried to modify your code for my data but ended up with FDR values which are 
always same i.e 0.9999609. Could you please tell me where I am doing wrong in 
the following code? You have explanined the pasila package but how will it be 
when I have two plain text files, where first column contains ensembl ids and 
second column contains counts? I have no solid R background and your help 
would be appreciated.
Thanks!


directory<-"~/Kisun/Data/Untrimmed/Deseq/extdata"
sampleFiles<-list.files(directory)
sampleCondition<-c("Untreated","Treated")
sampleTable<-data.frame(sampleName=sampleFiles, fileName=sampleFiles, 
condition=sampleCondition)
ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, 
directory=directory, design=~condition)
colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, 
levels=c("Untreated", "Treated"))
ddsHTSeq
dds<-DESeq(ddsHTSeq)
res<-results(dds)
res<-res[order(res$FDR),]
head(res)

Kind Regards
Kisun

-- 
Kisun Pokharel, M.Sc.
MTT Agrifood Research Finland
Biotechnology and Food Research
Myllytie 1, FI-31600 Jokioinen
+358503614763
mtt.fi/experts/kisun_pokharel[1]
twitter.com/kisunpokharel[2] 

--------
[1] mtt.fi/experts/kisun_pokharel
[2] twitter.com/kisunpokharel

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