[BioC] mas5calls Problem

Lizhe Xu lxu at chnola-research.org
Wed Mar 24 17:34:32 CET 2004

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 at hhc.eisai.co.jp [mailto:t-kawai at hhc.eisai.co.jp]
Sent: Tuesday, March 23, 2004 6:53 PM
To: Lizhe Xu
Subject: RE: mas5calls


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
 C:/Program Files/R/rw1081/9 3 396a.CEL C:/Program Files/R/rw1081/4 1
C:/Program Files/R/rw1081/4 2 342a.CEL C:/Program Files/R/rw1081/4 3



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 at hhc.eisai.co.jp

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