I am trying to run DEXSeq and I made all of the count files using your DEXSeq-Count which was successful. The factor I am comparing is "Condition" and factor level 1 is called "GFP" while factor level 2 is called "ICD". These are different variables of my condition. I entered in all of the correct data and I followed the example given on the DEXSeq galaxy page. I also prepared the annotation using DEXSeq-Count as well. However I get the same error every time I try to run the final step of DEXSeq on my conditions. Thank you for your help!
Here is the error message:
Warning message: In DESeqDataSet(rse, design, ignoreRank = TRUE) : some variables in design formula are characters, converting to factors using supplied model matrix Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) : all gene-wise dispersion estimates are within 2 orders of magnitude from the minimum value, and so the standard curve fitting techniques will not work. One can instead use the gene-wise estimates as final estimates: dds <- estimateDispersionsGeneEst(dds) dispersions(dds) <- mcols(dds)$dispGeneEst ...then continue with testing using nbinomWaldTest or nbinomLRT Calls: estimateDispersions ... estimateDispersions -> .local -> estimateDispersionsFit