David Tao | 20 Nov 01:47 2012

DESeq padj problem

Hi,Bioconductor team,
> I'm recently doing same work about RNA-seq DGE, I used bowtie2 to align
> the reads to reference trancriptome and used eXpress to generate
> the read counts, and the data has no biological replicates, the R
> command line is as follows, the padjs I get only have 1 and NA, where
> did I do wrong?
>  >countTable<-read.table("eXpresscountmatrix", header=T, row.names=1)
>  >condition<-factor(c("A1","A2","A3"))
>  > library( "DESeq" )
>  > cds = newCountDataSet( countTable, condition )
>  > cds = estimateSizeFactors( cds )
>  > cds = estimateDispersions( cds, method="blind", sharingMode="fit-only" )
>  > res_A1vsA2 = nbinomTest( cds, "A1", "A2" )
>  > res_A1vsA3 = nbinomTest( cds, "A1", "A3" )
>  > res_A2vsA3 = nbinomTest( cds, "A2", "A3" )
>  > resSig_A1vsA2 = res_A1vsA2[ res_A1vsA2$padj < 0.1, ]
>  > resSig_A1vsA3 = res_A1vsA3[ res_A1vsA3$padj < 0.1, ]
>  > resSig_A2vsA3 = res_A2vsA3[ res_A2vsA3$padj < 0.1, ]
> Thanks in advance!
> Tao

2012-11-20

David Tao
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