I’ve been struggling here for days now on attempting to get multiple factors to work in Galaxy for either EdgeR OR limma. I’ve searched every post about this and each says it’s a header issue. It is NOT a header issue. If I have only one factor and input the 5 separate groups within that one factor, each with it’s own count file it works fine and I can compare between each via contrasts. The count files have headers as GeneID for column1 and the unique sample name in column 2. However, when I attempt to add a separate Factor and include use the same files that worked in the previous step…I always get a duplicate row name error. I’ve tried even doing this via a count matrix file with all of the samples and counts…as well as a Factor info file; for both I followed the EXACT format as described on the package help section displayed if you scroll down. This did not work either.
Currently, I have absolutely no way to utilize the platform to peform DE analysis with the appropriate factor levels. Again, this is not a header issue with the counts files. I’ve tried this with both htseq counts (which I manually entered the header) AND featurecounts. These work fine if I only have one Factor level…as soon as I add an additional factor level it fails, despite being the exact same files that worked previously. I REALLY need help. I’d be greatly appreciative as my advisor needs this analysis for a grant application.