Hi, We tried expresso() in R, but with bad luck. >eset <- expresso(data, bgcorrect.method="mas", normalize.method="qspline", >pmcorrect.method="subtractmm", summary.method="playerout") background correction: mas normalization: qspline PM/MM correction : subtractmm expression values: playerout background correcting...done. normalizing...[1] "samples= 100 k= 5 first= 0" Error in rep(data, t1) : invalid number of copies in "rep" In addition: Warning message: 'k' found is non-sense. using default in: normalize.qspline(t(intensity(abatch)), ...) > In R we want to imitate the .CHP file we get from an .CEL file in Affymetrix Microarray Suite. Is there anyone that know how to tweek the parameters in expresso() to reach that result? Best regards Daniel Marcus

On Mon, Jun 16, 2003 at 03:50:59PM +0000, Daniel ~ wrote: > > Hi, > > We tried expresso() in R, but with bad luck. Some people associate luck good or bad with numbers... Could we know what are the version numbers for both R and the package 'affy' ? > > >eset <- expresso(data, bgcorrect.method="mas", normalize.method="qspline", > >pmcorrect.method="subtractmm", summary.method="playerout") > background correction: mas > normalization: qspline > PM/MM correction : subtractmm > expression values: playerout > background correcting...done. > normalizing...[1] "samples= 100 k= 5 first= 0" > Error in rep(data, t1) : invalid number of copies in "rep" > In addition: Warning message: > 'k' found is non-sense. using default in: > normalize.qspline(t(intensity(abatch)), ...) > > > > > In R we want to imitate the .CHP file we get from an .CEL file in > Affymetrix Microarray Suite. Is there anyone that know how to tweek > the parameters in expresso() to reach that result? There is no parameter I know of that would do that. However, other functions (eventually added by snippets of R code you made) should let you have what you want. Hopin' it helps, L.

i dont fully understand your email, but im guessing the function mas5 may be what you are looking for. mas5 basically does expresso(data,bgcorrect.method="mas",pmcorrect.method="mas", normalize=FALSE,summary.method="mas",...) but it also normalizes using the function: affy.scalevalue.exprSet rafael ps - data is a function in R's base package. i prefer using Data or mydata. On Mon, 16 Jun 2003, Daniel ~ wrote: > > Hi, > > We tried expresso() in R, but with bad luck. > > >eset <- expresso(data, bgcorrect.method="mas", normalize.method="qspline", > >pmcorrect.method="subtractmm", summary.method="playerout") > background correction: mas > normalization: qspline > PM/MM correction : subtractmm > expression values: playerout > background correcting...done. > normalizing...[1] "samples= 100 k= 5 first= 0" > Error in rep(data, t1) : invalid number of copies in "rep" > In addition: Warning message: > 'k' found is non-sense. using default in: > normalize.qspline(t(intensity(abatch)), ...) > > > > > In R we want to imitate the .CHP file we get from an .CEL file in > Affymetrix Microarray Suite. Is there anyone that know how to tweek > the parameters in expresso() to reach that result? > > Best regards > Daniel Marcus > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >