I really don't know if there is a problem or not for the background correction. I don't have anything to compare with it, at least there is no error displayed on the screen. For the flag, since I have a filter results on flag from Affy DMT, I compared it with the output of the Affy package and found the problem. Do you know other possible reasons for the inconsistant result provided by mas5calls command? Thanks for the explain of the "337a", "395a", "396a", "338a", "342a","341a". I did not realize these numbers coming from my samples. They were attached by our Microarray core lab, I refer them as 9-1, 9-2, ...4-2, 4-3, L Xu -----Original Message----- From: t-kawai@hhc.eisai.co.jp [mailto:t-kawai@hhc.eisai.co.jp] Sent: Tuesday, March 23, 2004 6:53 PM To: Lizhe Xu Subject: RE: mas5calls Hi, Sorry, my suggestion missed the point. How about the background correction? Following script works? > Data<-ReadAffy() > Data2 <- bg.correct.mas5(Data) > Dataf<-mas5calls(Data2) 22283 ids to be processed ......... "colnames(exprs(Data)) ..." means > Data <- ReadAffy() > colnames(exprs(Data)) <- c(") > Dataf<-mas5calls(Data) 22283 ids to be processed ......... > exprs(Dataf)[5870,] 337a 395a 396a 338a 342a 341a "A" "P" "A" "P" "M" "A" instead of > 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" bye. _______________________________________ Takatoshi Kawai, Ph.D. Senior Sientist, Bioinformatics Laboratoy of Seeds Finding Technology Eisai Co., Ltd. 5-1-3 Tokodai, Tsukuba-shi, Ibaraki 300-2635, Japan TEL: +81-29-847-7192 FAX: +81-29-847-7614 e-mail: t-kawai@hhc.eisai.co.jp