edgeR error running htseq-count files

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When I attempt to run edgeR under default conditions with successfully processed htseq-count files, I get fatal error: exit code 1 ():

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

Not sure what this means. I’m trying to analyze two htseq-count files from different treatment conditions. Both look fine on their own.

Any help would be appreciated.

Thanks,
Nick

1 Like
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hi @npokorzynski

This also looks like an input problem. See the first question you asked for more help: DESeq2 error running htseq-count

Closing this Topic out so we can keep the conversation (almost certainly the same input problem with both tools) in the same thread for context.

Thanks!