Dear List I have a cDNA microarray data set with 33696 probes and 36 arrays Variables defined in RG$target are names(RG$targets) [1] "ShortName" "pRed" "pGreen" "IDRed" "IDGreen" [6] "cdiff" "experiment" "pRed" indicates what type of samples that are labelled with the red dye (two different types of samples) "experiment" indicates in which experiment (1 or 2) the array was run. I have used arrayQualityMetrics for quality control. The command I have run before is this arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("pRed","experiment"), force = TRUE) this worked fine I know want to redo the analysis, but with intgroup = c("experiment","pRed") instead to get different colouring in pca plot and heatmap diagram So I tried this command: arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("experiment","pRed"), force = TRUE) and the computer was running and running ... then I tried arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("experiment","pRed"), force = TRUE,spatial = FALSE) and the computer was running and running ... I let this go for approximately half a day and one night and then stopped it. I don't really know how much time this took the first time I ran the command, but I am sure that I did not wait for a very long time. Moreover it is only the heatmap, pca plots and box plots that will be different so how can I generate these without doing the complete analysis? Ingunn > sessionInfo() R version 2.11.0 (2010-04-22) i686-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] MASS_7.3-5 convert_1.24.0 [3] marray_1.26.0 ggplot2_0.8.7 [5] digest_0.4.2 reshape_0.8.3 [7] plyr_0.1.9 proto_0.3-8 [9] arrayQualityMetrics_2.6.0 affyPLM_1.24.0 [11] preprocessCore_1.10.0 gcrma_2.20.0 [13] affy_1.26.1 Biobase_2.8.0 [15] limma_3.4.3 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.0 AnnotationDbi_1.10.1 [4] beadarray_1.16.0 Biostrings_2.16.5 DBI_0.2-5 [7] genefilter_1.30.0 hwriter_1.2 IRanges_1.6.6 [10] lattice_0.18-5 latticeExtra_0.6-11 RColorBrewer_1.0-2 [13] RSQLite_0.9-1 simpleaffy_2.24.0 stats4_2.11.0 [16] survival_2.35-8 tools_2.11.0 vsn_3.16.0 [19] xtable_1.5-6 > Ingunn Berget (Dr. Scient) UMB, box 5003, IHA 1432 ?s Norway Centre for Integrative Genetics, www.cigene.no Centre for Biospectroscopy and Data Modelling, www.specmod.org

Dear Ingunn, Can you please show the content of the column "experiment"? Apparently this is the cause of the failure. Also, if you are just interested in re-running the PCA with the colouring accordingly to "experiment" instead of "pRed", you can just use the function aqm.predata() and subsequently aqm.pca(). Best wishes, Audrey 2010/7/1 Ingunn Berget <ingunn.berget at="" umb.no="">: > Dear List > > I have a cDNA microarray data set with 33696 probes and 36 arrays > Variables defined in RG$target are > > names(RG$targets) > [1] "ShortName" ?"pRed" ? ? ? "pGreen" ? ? "IDRed" ? ? ?"IDGreen" > [6] "cdiff" ? ? ?"experiment" > > "pRed" indicates what type of samples that are labelled with the red dye (two different types of samples) > "experiment" indicates in which experiment (1 or 2) the array was run. > > I have used arrayQualityMetrics for quality control. > > The command I have run before is this > > arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("pRed","experiment"), force = TRUE) > > this worked fine > > I know want to redo the analysis, but with intgroup = c("experiment","pRed") instead to get different colouring in pca plot and heatmap diagram > > So I tried this command: > arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("experiment","pRed"), force = TRUE) > > and the computer was running and running ... > > then I tried > > arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("experiment","pRed"), force = TRUE,spatial = FALSE) > > and the computer was running and running ... > > I let this go for approximately half a day and one night and then stopped it. > I don't really know how much time this took the first time I ran the command, but I am sure that I did not wait for a very long time. > Moreover it is only the heatmap, pca plots and box plots that will be different so how can I generate these without doing the complete analysis? > > Ingunn > >> sessionInfo() > R version 2.11.0 (2010-04-22) > i686-pc-linux-gnu > > locale: > ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 > ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] splines ? grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets > [8] methods ? base > > other attached packages: > ?[1] MASS_7.3-5 ? ? ? ? ? ? ? ?convert_1.24.0 > ?[3] marray_1.26.0 ? ? ? ? ? ? ggplot2_0.8.7 > ?[5] digest_0.4.2 ? ? ? ? ? ? ?reshape_0.8.3 > ?[7] plyr_0.1.9 ? ? ? ? ? ? ? ?proto_0.3-8 > ?[9] arrayQualityMetrics_2.6.0 affyPLM_1.24.0 > [11] preprocessCore_1.10.0 ? ? gcrma_2.20.0 > [13] affy_1.26.1 ? ? ? ? ? ? ? Biobase_2.8.0 > [15] limma_3.4.3 > > loaded via a namespace (and not attached): > ?[1] affyio_1.16.0 ? ? ? ?annotate_1.26.0 ? ? ?AnnotationDbi_1.10.1 > ?[4] beadarray_1.16.0 ? ? Biostrings_2.16.5 ? ?DBI_0.2-5 > ?[7] genefilter_1.30.0 ? ?hwriter_1.2 ? ? ? ? ?IRanges_1.6.6 > [10] lattice_0.18-5 ? ? ? latticeExtra_0.6-11 ?RColorBrewer_1.0-2 > [13] RSQLite_0.9-1 ? ? ? ?simpleaffy_2.24.0 ? ?stats4_2.11.0 > [16] survival_2.35-8 ? ? ?tools_2.11.0 ? ? ? ? vsn_3.16.0 > [19] xtable_1.5-6 >> > > > > Ingunn Berget (Dr. Scient) > UMB, box 5003, IHA > 1432 ?s > Norway > > Centre for Integrative Genetics, www.cigene.no > Centre for Biospectroscopy and Data Modelling, www.specmod.org > > _______________________________________________ > 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 > -- Audrey Kauffmann Bergonie Cancer Institute 229 Cours de l'Argonne 33076 Bordeaux France