I am analyzing FPKM RNA-seq data downloaded from DGC database. Now trying to identify genes that differently expressed between sanmples by conducting DESeqDataSetFromHTSeqCount. But I got an error saying:

Error in DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, : Gene IDs (first column) differ between files.

And I don`t know hot to figure it out and need suggestions. Here is the commands I have done.

`

setwd("~/Download/GC/FPKMs") directory <- "~/Download/GC/FPKMs" library(DESeq2) sampletable <- data.frame(sampleName = samplesheet$path, fileName = samplesheet$path, condition=samplesheet$label) sampletable

       sampleName          fileName condition

1 ECsample1.txt ECsample1.txt 1 2 ECsample2.txt ECsample2.txt 0 3 ECsample3.txt ECsample3.txt 1

[ reached 'max' / getOption("max.print") -- omitted 249 rows ]

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable, directory = directory, design= ~ condition)

Error in DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, : Gene IDs (first column) differ between files.

`

The content of each sample file is like:

ENSG00000242268.2 0.0 ENSG00000270112.3 0.00258202876781 ENSG00000167578.15 3.30893315419 ENSG00000273842.1 0.0 ENSG00000078237.5 8.05933601781 ENSG00000146083.10 15.0446810186 ENSG00000225275.4 0.0 ENSG00000158486.12 0.221675972087

Could you give me an advice what kind of data and format I need? Thank you!

I am analyzing FPKM RNA-seq data

This never ends well. FPKM is unsuitable for DESeq. It wants raw counts only. If you lie and pretend that's what you have when it's not, you can't trust your results.