Dear Communities, The series matrix of GSE148160 downloaded directly from GEO database showing negative value. So CEL files were processed by oligo package. The value of affyRaw showed non-negative value (attached figure). But there was negative value after oligo::rma procedure (attached figure). In my opinion, the negative value should not be got after rma only if the data was scale or center to zero further. Could you please explain this to me? Thanks so much!
affyRaw <- oligo::read.celfiles(celFiles) summary(exprs(affyRaw)) eset <- oligo::rma(object = affyRaw) summary(exprs(eset))