Dear Ben and list, I have just rerun my code and now it works fine. Sorry for bothering, there was probably some typo. Regards, David > Below is my results using affyPLM 1.9.5. No particular problem here > with that version. What was your fitPLM call? > > > > > > > > > Pset <- fitPLM(Dilution) > Background correcting PM > Normalizing PM > Fitting models > > NUSE(Pset,main="NUSE values",col=rainbow(4)) > > NUSE(Pset,type="stats") > 20A 20B 10A 10B > median 0.99929158 0.99939860 1.00213287 0.99927522 > IQR 0.02592881 0.02963567 0.02816327 0.02591606 > > NUSE(Pset,type="stats") > 20A 20B 10A 10B > median 0.99929158 0.99939860 1.00213287 0.99927522 > IQR 0.02592881 0.02963567 0.02816327 0.02591606 > > On Thu, 2006-06-15 at 13:11 +0200, kfbargad at ehu.es wrote: > > Dear list, > > > > I am using affyPLM for my QC, and am trying to obtain the median of > > the NUSE values for my chips. > > > > if I type > > >NUSE(Pset, main = "NUSE values") > > I get the NUSE boxplot > > > > but if I type > > > NUSE(Pset, type = "stats") > > Error in match.arg(type) : 'arg' should be one of plot, values > > or > > > NUSE(Pset, type = "values") > > Error in x at weights[which, ] : incorrect number of dimensions > > In addition: Warning messages: > > 1: longer object length > > is not a multiple of shorter object length in: model == (PM ~ - > > 1 + probes + samples) > > 2: longer object length > > is not a multiple of shorter object length in: model == (PM ~ - > > 1 + samples + probes) > > 3: the condition has length > 1 and only the first element will be > > used in: if ((model == (PM ~ -1 + probes + samples)) | (model == (PM ~ > > > > my sessionInfo() > > Version 2.3.0 (2006-04-24) > > i386-pc-mingw32 > > > > attached base packages: > > [1] "stats" "graphics" "grDevices" "utils" "datasets" "tools" > > "methods" "base" > > > > other attached packages: > > hgu133plus2cdf affyPLM gcrma matchprobes > > affydata affy affyio Biobase > > "1.12.0" "1.8.0" > > > > > > Any suggestions?? > > > > Also, is it possible to colour the boxes of the boxplot? I have so far > > been using > > boxplot() for Pset with the argument "col", but it does not work for > > NUSE() > > > > > > Thanks in advance, > > > > David > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- > Ben Bolstad <bmb at="" bmbolstad.com=""> > http://bmbolstad.com > >