In Galaxy it says Deseq is using count tables for each sample from htseq-count.
I want to feed Deseq with custom count tables (not generated from htseq-count) but it gives me error.
The tables are tab formatted as this, and each sample have same ids:
So probably I'm going something not as Deseq is especting :)
the error I got from Galaxy:
Warning message: In
*tmp*, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels in factors are deprecated
Error in DESeqDataSet(se, design = design, ignoreRank) :
design has a single variable, with all samples having the same value.
use instead a design of '~ 1'. estimateSizeFactors, rlog and the VST can then be used
Calls: DESeqDataSetFromHTSeqCount -> DESeqDataSetFromMatrix -> DESeqDataSet