Hello,
I want to do differential expression analysis with Galaxy, I have 129 samples that include normal and diseased.
I upload three files of count data, factor data and annodata, but when I run limma tools, I get this error.
I checked the factor data and it is similar to the count data.
Please guide me, thanks.
Error: Sample IDs in counts and factors files don’t match
Welcome, @Roya
You could double check that all 129 samples have matching labels.
I’ve also seen this come up when a file has a few extra columns without any labels at the end (can happen during file conversions if extra whitespace was not trimmed). Scroll over to the far right side of a tabular file to visually see that.
From here, I’m wondering what happens if you rename each sample to start with a letter? Remember to make the change everywhere that sample name is used.
s129
s128
s127
Or however you want to do that. Why? The tool you are using was written in R, and R doesn’t like certain values to start with a number. Galaxy can sometimes help to work around that, but Galaxy can’t change the actual underlying tool of course! So, the best advice is to try to make the underlying tool happy if you get a weird error 
More help → FAQ: Extended Help for Differential Expression Analysis Tools