When I am running the DESeq pipeline on the dds object and getting this error message.
> dds_res<-DESeq(dds_PvsN) estimating size factors Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot compute log geometric means In addition: Warning message: In class(object) <- "environment" : Setting class(x) to "environment" sets attribute to NULL; result will no longer be an S4 object
What strategy should be applied to resolve this conflict?
Thank you very much!
Thanks, Kevin and swbarnes2 for your replies,
Kevin your reply was the right solution. This helps us not to remove any sample during this analysis.
So adding a pseudo-count value of '1' to each entry in my data helps to resolve this error.
Best regards: Imran