I have been using DESeq2 to perform differential gene expression analysis between two groups but I do not have house keeping genes in the data set. Is it still possible to do DESeq calculations without the house keeping genes? and I do not have all the genes expressed across all subjects/samples.
I have the following error message calculating size factors:
dds <- DESeq(dds)
estimating size factors
Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, :
every gene contains at least one zero, cannot compute log geometric means
Any help would be appreciated.