Dear All,

I have 5 RNA-Seq experiments  and I want to compare the expression values. I have the raw counts. How
can normalize using deseq2? I can't draw any design on this because there is no meaning.

What do you suggest ?
Thanks in advance for any help

If you only want to compare across samples (not across genes), do this (you have to make up an empty column data):

coldata = DataFrame(row.names=1:ncol(counts))
dds = DESeqDataSetFromMatrix(counts, coldata, ~ 1)
dds = estimateSizeFactors(dds)
counts(dds, normalized=TRUE)

(edit) but this leads me to wonder: what are you trying to do with these normalized counts?

These samples are create after subsampling one big RNASeq experiments. I want to be sure the proportion of the expression are the same. So, the simple way is to verify if the  gene I'm studing are remain with the same ratio.

Thanks for the help!!