Hi

I was having some issues with the p-values of differential expression of my
samples using SAM, so I to compare with more traditional multiple testing
approaches
I thought I will just do a ttest and then use p.adjust to get  BH corrected
pvalues
My input is just a two column textfile where the first column is the Affy
probe IDs and the second is the ttest pvalue
All I get out is the same p-values I put in, since I am a pretty naive R
programmer I am sure there is something simple I am doing wrong

help will be greatly appreciated, thanks!!

here is my script:

Data<-read.table("input", header=TRUE, row.names=1)
p.adj    <- p.adjust(Data, method = "BH", n= length (Data))
write.table(p.adj, file="output", sep="\t")

My output is identical to my input

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