Hi,
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:
Contig_000039 159
Contig_000040 49
Contig_000041 4
Contig_000042 6
Contig_000043 2
Contig_000044 0
Contig_000045 2
Contig_000046 2
So probably I'm going something not as Deseq is especting :)
PS
the error I got from Galaxy:
Warning message:
In levels<-(*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
