edgeR cannot run

Hi all,

I have a RNA-seq have no replicates, so I am using edgeR to do DE. and I got counts data from featurecount. I run edgeR, but keep turning red… the warning message see below.
Could anyone help me with that?

Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Warning message:
In estimateDisp.default(y = y$counts, design = design, group = group, :
No residual df: setting dispersion to NA
Error in plotMDS.default(y, top = top, labels = labels, pch = pch, cex = cex, :
Only 2 columns of data: need at least 3
Calls: plotMDS → plotMDS.DGEList → plotMDS → plotMDS.default

1 Like

hi @Jiahui
it seems you have only two samples, while the latest versions of edgeR require replicates, hence “Only 2 columns of data: need at least 3”. The best option is to have replicates, at least for one condition. Alternatives: old versions might support analysis without replicates. Try an earlier versions of DESeq2 and/or edgeR. Cuffdiff supports analysis without replicates, at least old versions did.
Hope this helps.
Kind regards,