Hi BioC, I was suffering with this problem so followed the conversation which led to a conclusion last week. I have installed version 2.4.1 this morning. I like to run the arrayQualityMetrics on both the raw and Normalised data. The normalised data runs fine and I'm happy to report the labelling issue has been resolved. However, something odd has occurred which I can't track. > arrayQualityMetrics(rg, "QCReport_20mg", force=TRUE,do.logtransform = TRUE,intgroup="Cy5", grouprep=TRUE) The report will be written in directory 'QCReport_20mg'. Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent > arrayQualityMetrics(ma, "QCReportMA_20mg", force=TRUE,do.logtransform = FALSE,intgroup="Cy5", grouprep=TRUE) The report will be written in directory 'QCReportMA_20mg'. [[1]] [[2]] [[3]] The raw data now reports an error but the normalised data does not. This code used to run fine so I'm not sure what has changed in the new version to prevent it. traceback shows traceback() 7: `colnames<-`(`*tmp*`, value = 1:4) 6: aqm.prepdata(expressionset, do.logtransform) 5: aqm.prepdata(expressionset, do.logtransform) 4: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, intgroup, grouprep) 3: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, intgroup, grouprep) 2: arrayQualityMetrics(rg, "QCReport_20mg", force = TRUE, do.logtransform = TRUE, intgroup = "Cy5", grouprep = TRUE) 1: arrayQualityMetrics(rg, "QCReport_20mg", force = TRUE, do.logtransform = TRUE, intgroup = "Cy5", grouprep = TRUE) Session Info R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] convert_1.20.0 marray_1.22.0 limma_2.18.3 arrayQualityMetrics_2.4.1 affyPLM_1.20.0 preprocessCore_1.6.0 [7] gcrma_2.16.0 Biostrings_2.12.10 IRanges_1.2.3 affy_1.22.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affyio_1.12.0 annotate_1.22.0 AnnotationDbi_1.6.1 beadarray_1.12.1 DBI_0.2-4 genefilter_1.24.3 grid_2.9.0 hwriter_1.1 [9] KernSmooth_2.23-3 lattice_0.17-26 latticeExtra_0.6-4 RColorBrewer_1.0-2 RSQLite_0.7-3 simpleaffy_2.20.0 splines_2.9.0 stats4_2.9.0 [17] survival_2.35-7 tools_2.9.0 vsn_3.12.0 xtable_1.5-5 I think it may be related to my annotation of the files when assigning targets which I do here targets <- readTargets(file="Targets.txt", row.names="Filename") Here is the file Filename Cy5 Cy3 US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_1.txt AL-C1D21 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_2.txt AL-C1D21 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_3.txt AL-C1D21 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_4.txt AL-C1D1 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_1.txt CGE-C2D21 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_2.txt CGE-C1D1 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_3.txt CGE-C1D1 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_4.txt CGE-C1D1 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_1.txt BS-C1D1 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_2.txt BS-C1D1 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_3.txt CGE-C2D21 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_4.txt CGE-C2D21 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_1.txt BS-C1D21 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_2.txt BS-C1D21 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_3.txt BS-C1D21 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_4.txt BS-C1D1 ref US91903684_252414410017_S01_GE2_105_Dec08_2_EH_2_1.txt AL-C1D1 ref US91903684_252414410017_S01_GE2_105_Dec08_2_EH_2_2.txt AL-C1D1 ref Can anyone help resolve this? Thanks Elliott This message has been scanned for viruses by BlackSpider...{{dropped:3}}

Hi Elliott, I did not manage to reproduce the error you got, so I have a few questions. Is the object rg an RGList? Does it have 4 channels (red foreground and background and green foreground and background)? Can you show how you go from rg to ma? Hopefully I will be able to understand better what is going on and find out what went wrong (I never saw such error before). Thank you for your feedback, it is always useful to track down errors. Best wishes, Audrey > Hi BioC, > > I was suffering with this problem so followed the conversation which led to a conclusion last week. > I have installed version 2.4.1 this morning. > I like to run the arrayQualityMetrics on both the raw and Normalised data. > The normalised data runs fine and I'm happy to report the labelling issue has been resolved. > However, something odd has occurred which I can't track. > >> arrayQualityMetrics(rg, "QCReport_20mg", force=TRUE,do.logtransform = > TRUE,intgroup="Cy5", grouprep=TRUE) > The report will be written in directory 'QCReport_20mg'. > Error in dimnames(x) <- dn : > length of 'dimnames' [2] not equal to array extent >> arrayQualityMetrics(ma, "QCReportMA_20mg", force=TRUE,do.logtransform > = FALSE,intgroup="Cy5", grouprep=TRUE) > The report will be written in directory 'QCReportMA_20mg'. > [[1]] > > [[2]] > > [[3]] > > > The raw data now reports an error but the normalised data does not. > > > This code used to run fine so I'm not sure what has changed in the new version to prevent it. > > traceback shows > > traceback() > 7: `colnames<-`(`*tmp*`, value = 1:4) > 6: aqm.prepdata(expressionset, do.logtransform) > 5: aqm.prepdata(expressionset, do.logtransform) > 4: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, > intgroup, grouprep) > 3: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, > intgroup, grouprep) > 2: arrayQualityMetrics(rg, "QCReport_20mg", force = TRUE, > do.logtransform = TRUE, > intgroup = "Cy5", grouprep = TRUE) > 1: arrayQualityMetrics(rg, "QCReport_20mg", force = TRUE, > do.logtransform = TRUE, > intgroup = "Cy5", grouprep = TRUE) > > > Session Info > > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] convert_1.20.0 marray_1.22.0 limma_2.18.3 > arrayQualityMetrics_2.4.1 affyPLM_1.20.0 preprocessCore_1.6.0 > > [7] gcrma_2.16.0 Biostrings_2.12.10 IRanges_1.2.3 > affy_1.22.1 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 annotate_1.22.0 AnnotationDbi_1.6.1 > beadarray_1.12.1 DBI_0.2-4 genefilter_1.24.3 grid_2.9.0 hwriter_1.1 > [9] KernSmooth_2.23-3 lattice_0.17-26 latticeExtra_0.6-4 > RColorBrewer_1.0-2 RSQLite_0.7-3 simpleaffy_2.20.0 > splines_2.9.0 stats4_2.9.0 > [17] survival_2.35-7 tools_2.9.0 vsn_3.12.0 > xtable_1.5-5 > > > I think it may be related to my annotation of the files when assigning targets which I do here > > targets <- readTargets(file="Targets.txt", row.names="Filename") > > Here is the file > > Filename Cy5 Cy3 > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_1.txt AL- C1D21 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_2.txt AL- C1D21 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_3.txt AL- C1D21 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_4.txt AL- C1D1 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_1.txt CGE-C2D21 ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_2.txt CGE- C1D1 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_3.txt CGE- C1D1 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_4.txt CGE- C1D1 > ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_1.txt BS- C1D1 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_2.txt BS-C1D1 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_3.txt CGE-C2D21 ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_4.txt CGE- C2D21 ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_1.txt BS- C1D21 > ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_2.txt BS- C1D21 > ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_3.txt BS- C1D21 > ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_4.txt BS- C1D1 ref US91903684_252414410017_S01_GE2_105_Dec08_2_EH_2_1.txt AL-C1D1 ref US91903684_252414410017_S01_GE2_105_Dec08_2_EH_2_2.txt AL-C1D1 ref > > > Can anyone help resolve this? > > Thanks > > Elliott > > > This message has been scanned for viruses by BlackSpider...{{dropped:3}} > > _______________________________________________ > 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 EMBL - EBI Cambridge UK +44 (0) 1223 492 631 http://www.ebi.ac.uk/~audrey

HI Audrey, Thanks for getting back to me. rg is an rglist with 4 channels > class(rg) [1] "RGList" attr(,"package") [1] "limma" > summary(rg) Length Class Mode G 1133568 -none- numeric Gb 1133568 -none- numeric R 1133568 -none- numeric Rb 1133568 -none- numeric targets 3 data.frame list genes 11 data.frame list source 1 -none- character printer 4 -none- list This is the procedure used to get from rg to ma rgb <- backgroundCorrect(rg, method="normexp",offset=50) ma <- normalizeWithinArrays(rgb, method="loess") ma <- normalizeBetweenArrays(ma, method="quantile") Hope that helps Thanks Elliott -----Original Message----- From: Audrey Kauffmann [mailto:audrey@ebi.ac.uk] Sent: 03 November 2009 12:05 To: elliott harrison Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] ArrayQualityMetrics: Problem with labels in plots Hi Elliott, I did not manage to reproduce the error you got, so I have a few questions. Is the object rg an RGList? Does it have 4 channels (red foreground and background and green foreground and background)? Can you show how you go from rg to ma? Hopefully I will be able to understand better what is going on and find out what went wrong (I never saw such error before). Thank you for your feedback, it is always useful to track down errors. Best wishes, Audrey > Hi BioC, > > I was suffering with this problem so followed the conversation which led to a conclusion last week. > I have installed version 2.4.1 this morning. > I like to run the arrayQualityMetrics on both the raw and Normalised data. > The normalised data runs fine and I'm happy to report the labelling issue has been resolved. > However, something odd has occurred which I can't track. > >> arrayQualityMetrics(rg, "QCReport_20mg", force=TRUE,do.logtransform = > TRUE,intgroup="Cy5", grouprep=TRUE) > The report will be written in directory 'QCReport_20mg'. > Error in dimnames(x) <- dn : > length of 'dimnames' [2] not equal to array extent >> arrayQualityMetrics(ma, "QCReportMA_20mg", force=TRUE,do.logtransform > = FALSE,intgroup="Cy5", grouprep=TRUE) > The report will be written in directory 'QCReportMA_20mg'. > [[1]] > > [[2]] > > [[3]] > > > The raw data now reports an error but the normalised data does not. > > > This code used to run fine so I'm not sure what has changed in the new version to prevent it. > > traceback shows > > traceback() > 7: `colnames<-`(`*tmp*`, value = 1:4) > 6: aqm.prepdata(expressionset, do.logtransform) > 5: aqm.prepdata(expressionset, do.logtransform) > 4: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, > intgroup, grouprep) > 3: arrayQualityMetrics(expressionset, outdir, force, do.logtransform, > intgroup, grouprep) > 2: arrayQualityMetrics(rg, "QCReport_20mg", force = TRUE, > do.logtransform = TRUE, > intgroup = "Cy5", grouprep = TRUE) > 1: arrayQualityMetrics(rg, "QCReport_20mg", force = TRUE, > do.logtransform = TRUE, > intgroup = "Cy5", grouprep = TRUE) > > > Session Info > > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] convert_1.20.0 marray_1.22.0 limma_2.18.3 > arrayQualityMetrics_2.4.1 affyPLM_1.20.0 preprocessCore_1.6.0 > > [7] gcrma_2.16.0 Biostrings_2.12.10 IRanges_1.2.3 > affy_1.22.1 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 annotate_1.22.0 AnnotationDbi_1.6.1 > beadarray_1.12.1 DBI_0.2-4 genefilter_1.24.3 grid_2.9.0 hwriter_1.1 > [9] KernSmooth_2.23-3 lattice_0.17-26 latticeExtra_0.6-4 > RColorBrewer_1.0-2 RSQLite_0.7-3 simpleaffy_2.20.0 > splines_2.9.0 stats4_2.9.0 > [17] survival_2.35-7 tools_2.9.0 vsn_3.12.0 > xtable_1.5-5 > > > I think it may be related to my annotation of the files when assigning targets which I do here > > targets <- readTargets(file="Targets.txt", row.names="Filename") > > Here is the file > > Filename Cy5 Cy3 > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_1.txt AL- C1D21 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_2.txt AL- C1D21 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_3.txt AL- C1D21 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_4.txt AL- C1D1 ref US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_1.txt CGE-C2D21 ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_2.txt CGE- C1D1 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_3.txt CGE- C1D1 > ref > US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_4.txt CGE- C1D1 > ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_1.txt BS- C1D1 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_2.txt BS-C1D1 ref US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_3.txt CGE-C2D21 ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_4.txt CGE-C2D21 ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_1.txt BS- C1D21 > ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_2.txt BS- C1D21 > ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_3.txt BS- C1D21 > ref > US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_4.txt BS- C1D1 ref US91903684_252414410017_S01_GE2_105_Dec08_2_EH_2_1.txt AL-C1D1 ref US91903684_252414410017_S01_GE2_105_Dec08_2_EH_2_2.txt AL-C1D1 ref > > > Can anyone help resolve this? > > Thanks > > Elliott > > > This message has been scanned for viruses by BlackSpider...{{dropped:3}} > > _______________________________________________ > 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 EMBL - EBI Cambridge UK +44 (0) 1223 492 631 http://www.ebi.ac.uk/~audrey This message has been scanned for viruses by BlackSpider...{{dropped:3}}