Error running edgeR DEG Please help.

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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

when I tried to run DEG by galaxy edgeR this error message shows up.

Transcript_ID MAL_Read_Count
NM_008515 1
NM_010399 10
NM_001004761 19
NM_001005864 15

Transcript_ID MAP_Read_Count
NM_008515 15
NM_010399 13
NM_001004761 12
NM_001005864 13

so I uploaded these two separate count files,
and for the factor, I used Genotype,
for the group 1, I used WT
for the group 2, I used MT
and for the contrast, I usded WT-MT

what is wrong with my input?

1 Like
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Hello @simon

Replicates are required and it looks as if you are only using one.

There could also be some formatting problem if you are uploading the data. Check to make sure the data is actually organized into tab-separated columns. You also need three columns of data with the setting you are using.

The tool form has more help. Also see:

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2 posts were split to a new topic: DEseq2 input format problem