I am now running Deseq2 analysis. However, I am stuck at extracting the results with results(dds, contrast = ()) after deseq() from the large DESeqDataSet. The problem was, it took me extremely long to only extract one comparison (3 hours/comparison meanwhile, I have 265 comparison to extract). I am planning to make a subset of the dds large matrix (after running the deseq()) since I don't want to lose genes before normalization. However, I always got an error when running results(dds, contrast = ()) using the new subset matrix :
Error in counts(object) %*% whichSamples : non-conformable arguments
Then, I tried to relevel the variable containing the numerator and denumerator for contrast function and it gave me another error :
Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues
It seems like the contrast = could not recognize the numerator and denumerator from the new subset matrix. I also read that actually releveling the factor after running the deseq() isn't allowed as it makes the software confused. https://support.bioconductor.org/p/102317/
If there is a way to do solve this problem, please share with me. Thanks in advance.