Hello
Our group revisited some old codes for microarray data analysis in our group. We re-ran the code in a system with old versions of r and affy and a system with the up-to-date versions. We are aware of some differences in results of rma normalization when using different versions of r, affy package (and Bioconductor may be also involved in). Some of the differences are noticed in the first decimal place. We would like to share our findings for your reference even though we have no idea how and why it happened. The following is the details of the tests.

Test data: GSE11001

#rma normalization
library(affy)
data <- ReadAffy()
eset <- rma(data)
write.exprs(eset, file="output.txt")

Environment and results: