Is the bg.correct method "mas" the same as the newest MAS5.0 one with a weighted local correction based on grid averages (as I suspect)? Does anyone have an opinion about this as compared to the "rma" default method for bg.correct? Stephen Henderson WIBR -----Original Message----- From: Ben Bolstad [mailto:bolstad@stat.berkeley.edu] Sent: Thursday, November 21, 2002 4:45 PM To: Pawel Herzyk Cc: bioconductor Subject: Re: [BioC] affy 1.1 - rma function The three step procedure you outline does the same thing with the caveat that the bg.correct.rma function implements the background correction step in a slightly different way from the correction carried in the c code (which duplicates the bg function in affy 1.0 releases). Ben > Hi there, > > I have a questions related to what the "rma" function actually does. > > Let assume that I have converted the probe level data stored in the "Data" object to the gene expression values using the following > > > eset <- rma(Data) > > If I wanted to get the same effect but wanted to do it step by step so that I could save the intermediate AffyBatch objects, then according to my understanding the closest to the above would be the following: > > > bg.corrected.Data <- bg.correct.rma(Data) > > norm.Data <- normalize(bg.corrected.Data) > > eset <- express(norm.Data,bg.correct=F,normalize.method=F,summary.stat=medianp olish) > > Obviously I won't get exactly the same numbers because "rma" is written in C, so the codes are different, but am I correct in thinking that the above three-step procedure does virtually the same as "rma"? > > Pawel > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager (wibr.mail@ucl.ac.uk). All files are scanned for viruses. **********************************************************************

On Thu, Nov 21, 2002 at 05:43:25PM -0000, Stephen Henderson wrote: > Is the bg.correct method "mas" the same as the newest MAS5.0 one with a > weighted local correction based on grid averages (as I suspect)? The "mas" flavor for bg correction is believed to be the same as the one in MAS5.0 (and we need to fix the man page "bg.correct" to mention that). > > Does anyone have an opinion about this as compared to the "rma" default > method for bg.correct? I think Rafael and Ben have something on the way about that... L. > > Stephen Henderson > WIBR > > > -----Original Message----- > From: Ben Bolstad [mailto:bolstad@stat.berkeley.edu] > Sent: Thursday, November 21, 2002 4:45 PM > To: Pawel Herzyk > Cc: bioconductor > Subject: Re: [BioC] affy 1.1 - rma function > > The three step procedure you outline does the same thing with the caveat > that the bg.correct.rma function implements the background correction > step in a slightly different way from the correction carried in the c > code (which duplicates the bg function in affy 1.0 releases). > > Ben > > > > > Hi there, > > > > I have a questions related to what the "rma" function actually does. > > > > Let assume that I have converted the probe level data stored in the "Data" > object to the gene expression values using the following > > > > > eset <- rma(Data) > > > > If I wanted to get the same effect but wanted to do it step by step so > that I could save the intermediate AffyBatch objects, then according to my > understanding the closest to the above would be the following: > > > > > bg.corrected.Data <- bg.correct.rma(Data) > > > norm.Data <- normalize(bg.corrected.Data) > > > eset <- > express(norm.Data,bg.correct=F,normalize.method=F,summary.stat=media npolish) > > > > Obviously I won't get exactly the same numbers because "rma" is written in > C, so the codes are different, but am I correct in thinking that the above > three-step procedure does virtually the same as "rma"? > > > > Pawel > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > ********************************************************************** > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they > are addressed. If you have received this email in error please notify > the system manager (wibr.mail@ucl.ac.uk). All files are scanned for viruses. > ********************************************************************** > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent