After using the rma, I used mas5calls to read the flag call from Affy U133A .txt file. But I was surprised to find that the mas5calls got quite different results compared to the original .txt file (798 inconsistance for 22283 probe sets for a group of 6 arrays, when comparing with the DMT). Is it something I did wrong or a bug for this command? Here is what I did: > library(affy) Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Synching your local package management information ... > Data<-ReadAffy() > pData(Data) sample 9 1 337a.CEL 1 9 2 395a.CEL 2 9 3 396a.CEL 3 4 1 338a.CEL 4 4 2 342a.CEL 5 4 3 341a.CEL 6 > rmaData<-rma(Data) Background correcting Normalizing Calculating Expression > Dataf<-mas5calls(Data) 22283 ids to be processed ......... > pData(Dataf) sample 9 1 337a.CEL 1 9 2 395a.CEL 2 9 3 396a.CEL 3 4 1 338a.CEL 4 4 2 342a.CEL 5 4 3 341a.CEL 6 > gn<-geneNames(Dataf) > gn[5870] [1] "206344_at" > gn[7686] [1] "208180_s_at" > exprs(Dataf)[5870,] C:/Program Files/R/rw1081/9 1 337a.CEL C:/Program Files/R/rw1081/9 2 395a.CEL "A" "P" C:/Program Files/R/rw1081/9 3 396a.CEL C:/Program Files/R/rw1081/4 1 338a.CEL "A" "P" C:/Program Files/R/rw1081/4 2 342a.CEL C:/Program Files/R/rw1081/4 3 341a.CEL "M" "A" > exprs(Dataf)[7686,] C:/Program Files/R/rw1081/9 1 337a.CEL C:/Program Files/R/rw1081/9 2 395a.CEL "M" "A" C:/Program Files/R/rw1081/9 3 396a.CEL C:/Program Files/R/rw1081/4 1 338a.CEL "A" "P" C:/Program Files/R/rw1081/4 2 342a.CEL C:/Program Files/R/rw1081/4 3 341a.CEL "M" "A" Here I took two probeset as example (out of 798): for 206344 in the original .txt file the flags are A, P, A, "A", M, A for 208180 in the original .txt file the flags are "P", A, A, P, "P", A Thanks. Lizhe