Hello All,

I am using DESeq for identify differentially expressed genes among a couple
of samples. At the end of the calculations i write the results to 3 files
as follow:

resSig <- res[ res$padj < .01, ]
write.table(resSig,"~DESeq\\All.txt")
write.table(resSig[ order( resSig$foldChange, -resSig$baseMean ), ]
,"~\\DESeq\\DownRegulated.txt")
write.table(resSig[ order( -resSig$foldChange, -resSig$baseMean ),
],"~\\DESeq\\UpRegulated.txt")

My question here is,

   - In the DESeq paper it is mentioned that the last two lines of code
   extracts the up and downregulated genes, So I'm thinking the sum of the
   number of genes in (DownRegulated.txt + UpRegulated.txt) should equals the
   number of genes with padj value < .01 in the file All.txt. But, that does
   not apply in my case as the numbers not even close. Any explanation or help
   is appreciated.


-- 
Thank you,

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