I have 192 .CEL files (chip: Affymetrix Human Clariom S HT ). If I apply the RMA using Affymetrix Expression Console software (Analysis: Gene Level - SST-RMA) or with the rma() function from the Oligo package in R Bioconductor, I get quite different results. In general, the log2 expression values I obtained with Affymetrix Expression Console are higher than the values from the Oligo package, although the pattern of expression levels per transcript is the same. What is the reason for this difference and how should I decide which of the two methods to use?
Here's an example of the expression levels of a transcript for the first 7 arrays:
TC0100006675.hg.1 9.96045562120938 10.0166037327827 10.2163252874566 10.0278834737392 9.79302430710618 9.74687422664869 9.86460893871565
Affymetrix Expression Console:
TC0100006675.hg.1 14.02148 14.2837 14.33652 14.2356 13.81137 13.6973 13.91579
With Oligo, I applied the rma() function on the entire data set, including all spike-ins/control probes. I'm not sure if that's the case in Affymetrix and if that's the correct way to do so.
Thank you for your reply!