while I figure out what solution to implement, I'd suggest using something along the lines of: pms = log2(pm(OligoRaw)) dens = oligo:::matDensity(pms) cols = darkColors(ncol(pms)) boxplot(as.data.frame(pms), range=0, col=cols) matplot(dens[["x"]], dens[["y"]], type="l", lwd=2, col=cols, xlab="log-intensity", ylab="density") b On Thu, May 20, 2010 at 4:36 PM, Mike Smith <grimbough at="" googlemail.com=""> wrote: > Hi Javier, > > You can get a boxplot of the geneFeatureSet and expression set objects > using: > > boxplot(log2(exprs(OligoRaw))) and boxplot(exprs(OligoEset)) respectively. > > If I do the first command without the log transformation it takes about > 10 minutes to plot for some reason, but it does still work. > > Mike Smith > > > Javier P?rez Florido wrote: >> >> Dear Benilton, >> Thanks again for your help. Detaching 'affy' makes it work. >> However, I'm trying to use boxplot and histogram. For raw data it says: >> >> > boxplot(OligoRaw) >> Error in validObject(.Object) : >> ?invalid class "ExpressionSet" object: featureNames differ between >> assayData and featureData >> Error in exprs(channel(eset, chns[i])) : >> ?error in evaluating the argument 'object' in selecting a method for >> function 'exprs' >> >> And for an expression set object: >> >> > boxplot(OligoEset) >> Error in .local(x, ...) : object 'nsamples' not found >> >> Do I have to detach any other package? >> >> Thanks again, >> Javier >> >> >> > sessionInfo() >> R version 2.11.0 (2010-04-22) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=Spanish_Spain.1252 ?LC_CTYPE=Spanish_Spain.1252 >> ?LC_MONETARY=Spanish_Spain.1252 >> [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? LC_TIME=Spanish_Spain.1252 >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> ?[1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1 >> ? ? AnnotationDbi_1.10.0 >> ?[4] limma_3.4.0 ? ? ? ? ? ? ? ? ? ? ? ? ?vsn_3.16.0 >> ? ? genefilter_1.30.0 >> ?[7] pd.hugene.1.0.st.v1_3.0.1 ? ? ? ? ? ?RSQLite_0.8-4 >> ? ? ?DBI_0.2-5 >> [10] oligo_1.12.0 ? ? ? ? ? ? ? ? ? ? ? ? oligoClasses_1.10.0 >> ? ? ?Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> ?[1] affxparser_1.20.0 ? ? affy_1.26.0 ? ? ? ? ? affyio_1.16.0 >> annotate_1.26.0 ? ? ? Biostrings_2.16.0 >> ?[6] grid_2.11.0 ? ? ? ? ? IRanges_1.6.0 ? ? ? ? lattice_0.18-5 >> ?preprocessCore_1.10.0 splines_2.11.0 >> [11] survival_2.35-8 ? ? ? tools_2.11.0 ? ? ? ? ?xtable_1.5-6 >> > >> >> >> On 19/05/2010 21:56, Benilton Carvalho wrote: >>> >>> detach affy and try again (when you loaded 'affy' you got a message >>> saying that oligo::probeNames was being masked). >>> >>> fyi: we do have ideas on how to solve this. >>> >>> b >>> >>> 2010/5/19 Javier P?rez Florido<jpflorido at="" gmail.com="">: >>> >>>> >>>> Dear list, >>>> Some time ago I used the oligo package to read and pre-process (rma) a >>>> set >>>> of Human Gene ST 1.0 CEL files and it was OK. >>>> >>>> Now, I have resumed my work and with the new version of oligo and R >>>> (below >>>> is my session info), the same code doesn't work (the new oligo vignette >>>> is >>>> quite different to the one I used before). I have downloaded first the >>>> pd.hugene.1.0.st package from bioconductor and then I built it myself >>>> (to >>>> check if it was a problem of the annotation package) and the same error >>>> appears: >>>> >>>> OligoRaw<-read.celfiles(filenames=list.celfiles()) >>>> OligoEset<-rma(OligoRaw,target="core") # It is a GeneFeatureSet object >>>> Error in function (classes, fdef, mtable) ?: >>>> ?unable to find an inherited method for function "probeNames", for >>>> signature >>>> "GeneFeatureSet" >>>> >>>> Any suggestions? >>>> Thanks, >>>> Javier >>>> >>>> >>>> R version 2.11.0 (2010-04-22) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> [1] LC_COLLATE=Spanish_Spain.1252 ?LC_CTYPE=Spanish_Spain.1252 >>>> ?LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C >>>> [5] LC_TIME=Spanish_Spain.1252 >>>> >>>> attached base packages: >>>> ?[1] grid ? ? ?tools ? ? tcltk ? ? stats ? ? graphics ?grDevices utils >>>> datasets ?methods ? base >>>> >>>> other attached packages: >>>> ?[1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1 >>>> ? RColorBrewer_1.0-2 >>>> ?[4] gplots_2.7.4 ? ? ? ? ? ? ? ? ? ? ? ? caTools_1.10 >>>> ? bitops_1.0-4.1 >>>> ?[7] gdata_2.8.0 ? ? ? ? ? ? ? ? ? ? ? ? ?gtools_2.6.2 >>>> ? oneChannelGUI_1.14.2 >>>> [10] RaExExonProbesetLocation_1.0.0 ? ? ? MoExExonProbesetLocation_1.0.0 >>>> ? HuExExonProbesetLocationHg19_0.0.2 >>>> [13] edgeR_1.6.2 ? ? ? ? ? ? ? ? ? ? ? ? ?IRanges_1.6.0 >>>> ? ?preprocessCore_1.10.0 >>>> [16] GOstats_2.14.0 ? ? ? ? ? ? ? ? ? ? ? graph_1.26.0 >>>> ? Category_2.14.0 >>>> [19] AnnotationDbi_1.10.0 ? ? ? ? ? ? ? ? tkWidgets_1.26.0 >>>> ? DynDoc_1.26.0 >>>> [22] widgetTools_1.26.0 ? ? ? ? ? ? ? ? ? affylmGUI_1.22.0 >>>> ? affyio_1.16.0 >>>> [25] affy_1.26.0 ? ? ? ? ? ? ? ? ? ? ? ? ?limma_3.4.0 >>>> ? ?pd.hugene.1.0.st.v1_0.0.1 >>>> [28] pdInfoBuilder_1.12.0 ? ? ? ? ? ? ? ? oligo_1.12.0 >>>> ? oligoClasses_1.10.0 >>>> [31] affxparser_1.20.0 ? ? ? ? ? ? ? ? ? ?RSQLite_0.8-4 >>>> ? ?DBI_0.2-5 >>>> [34] Biobase_2.8.0 >>>> >>>> loaded via a namespace: >>>> ?[1] annotate_1.26.0 ? Biostrings_2.16.0 genefilter_1.30.0 GO.db_2.4.1 >>>> GSEABase_1.10.0 ? RBGL_1.24.0 ? ? ? splines_2.11.0 >>>> ?[8] survival_2.35-8 ? XML_3.1-0 ? ? ? ? xtable_1.5-6 >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> >> > > _______________________________________________ > 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 >