Hi I'm trying to run arrayQualityMetrics and I keep getting an error message saying that the intgroup is missing. However, I am very clearly specifying the intgroup and it definitely exists in my phenodata. I'm working with mogene.1.0.st.v1 arrays. Please see my error message and a few lines of my phenodata below: Error message: > arrayQualityMetrics(expressionset = dat, intgroup="SampleID",outdir = "QC_test", force =TRUE, do.logtransform = TRUE); The directory 'QC_test' has been created. Error in match(x, table, nomatch = 0L) : argument "intgroup" is missing, with no default phenodata: > pData(dat) ChipType SampleID MouseStrain TumorOrigin 01_4T1_mouse1.CEL MoGene-1_0-st-v1 4T1_1 Balb/c Spontaneous 02_4T1_mouse2.CEL MoGene-1_0-st-v1 4T1_2 Balb/c Spontaneous 03_4T1_mouse3.CEL MoGene-1_0-st-v1 4T1_3 Balb/c Spontaneous 04_4T1_mouse4.CEL MoGene-1_0-st-v1 4T1_4 Balb/c Spontaneous 05_EMT-6_mouse1.CEL MoGene-1_0-st-v1 EMT6_1 Balb/c Spontaneous 06_EMT-6_mouse2.CEL MoGene-1_0-st-v1 EMT6_2 Balb/c Spontaneous Any suggestions on how to fix this will be appreciated. -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] affyPLM_1.38.0 preprocessCore_1.24.0 [3] gcrma_2.34.0 affy_1.40.0 [5] arrayQualityMetrics_3.18.0 pd.mogene.1.0.st.v1_3.8.0 [7] RSQLite_0.11.4 DBI_0.2-7 [9] oligo_1.26.0 Biobase_2.22.0 [11] oligoClasses_1.24.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affxparser_1.34.0 affyio_1.30.0 annotate_1.40.0 [4] AnnotationDbi_1.24.0 beadarray_2.12.0 BeadDataPackR_1.14.0 [7] BiocInstaller_1.12.0 Biostrings_2.30.1 bit_1.1-11 [10] Cairo_1.5-5 cluster_1.14.4 codetools_0.2-8 [13] colorspace_1.2-4 ff_2.2-12 foreach_1.4.1 [16] Formula_1.1-1 genefilter_1.44.0 GenomicRanges_1.14.4 [19] grid_3.0.2 Hmisc_3.13-0 hwriter_1.3 [22] IRanges_1.20.6 iterators_1.0.6 lattice_0.20-24 [25] latticeExtra_0.6-26 limma_3.18.7 plyr_1.8 [28] RColorBrewer_1.0-5 reshape2_1.2.2 setRNG_2011.11-2 [31] splines_3.0.2 stats4_3.0.2 stringr_0.6.2 [34] survival_2.37-4 SVGAnnotation_0.93-1 vsn_3.30.0 [37] XML_3.98-1.1 xtable_1.7-1 XVector_0.2.0 [40] zlibbioc_1.8.0 > -- Sent via the guest posting facility at bioconductor.org.

Dear Guest Thank you for the report. The vignette of the package contains examples where the ?intgroup? argument is used, and the package builds (http://bioconductor.org/checkResults/release/bioc-LATEST/#A). Since the only difference to your example is the dataset ?dat?, we would need to investigate that to understand how it could possibly create the problem you report. Would it be possible for you to send me your object and the code needed to reproduce the problem, starting from a fresh R session? Best wishes Wolfgang On 5 Feb 2014, at 23:18, guest [guest] <guest at="" bioconductor.org=""> wrote: > > Hi I'm trying to run arrayQualityMetrics and I keep getting an error message saying that the intgroup is missing. However, I am very clearly specifying the intgroup and it definitely exists in my phenodata. I'm working with mogene.1.0.st.v1 arrays. Please see my error message and a few lines of my phenodata below: > > Error message: > >> arrayQualityMetrics(expressionset = dat, intgroup="SampleID",outdir = "QC_test", force =TRUE, do.logtransform = TRUE); > The directory 'QC_test' has been created. > Error in match(x, table, nomatch = 0L) : > argument "intgroup" is missing, with no default > > phenodata: > >> pData(dat) > ChipType SampleID MouseStrain TumorOrigin > 01_4T1_mouse1.CEL MoGene-1_0-st-v1 4T1_1 Balb/c Spontaneous > 02_4T1_mouse2.CEL MoGene-1_0-st-v1 4T1_2 Balb/c Spontaneous > 03_4T1_mouse3.CEL MoGene-1_0-st-v1 4T1_3 Balb/c Spontaneous > 04_4T1_mouse4.CEL MoGene-1_0-st-v1 4T1_4 Balb/c Spontaneous > 05_EMT-6_mouse1.CEL MoGene-1_0-st-v1 EMT6_1 Balb/c Spontaneous > 06_EMT-6_mouse2.CEL MoGene-1_0-st-v1 EMT6_2 Balb/c Spontaneous > > > Any suggestions on how to fix this will be appreciated. > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] affyPLM_1.38.0 preprocessCore_1.24.0 > [3] gcrma_2.34.0 affy_1.40.0 > [5] arrayQualityMetrics_3.18.0 pd.mogene.1.0.st.v1_3.8.0 > [7] RSQLite_0.11.4 DBI_0.2-7 > [9] oligo_1.26.0 Biobase_2.22.0 > [11] oligoClasses_1.24.0 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.34.0 affyio_1.30.0 annotate_1.40.0 > [4] AnnotationDbi_1.24.0 beadarray_2.12.0 BeadDataPackR_1.14.0 > [7] BiocInstaller_1.12.0 Biostrings_2.30.1 bit_1.1-11 > [10] Cairo_1.5-5 cluster_1.14.4 codetools_0.2-8 > [13] colorspace_1.2-4 ff_2.2-12 foreach_1.4.1 > [16] Formula_1.1-1 genefilter_1.44.0 GenomicRanges_1.14.4 > [19] grid_3.0.2 Hmisc_3.13-0 hwriter_1.3 > [22] IRanges_1.20.6 iterators_1.0.6 lattice_0.20-24 > [25] latticeExtra_0.6-26 limma_3.18.7 plyr_1.8 > [28] RColorBrewer_1.0-5 reshape2_1.2.2 setRNG_2011.11-2 > [31] splines_3.0.2 stats4_3.0.2 stringr_0.6.2 > [34] survival_2.37-4 SVGAnnotation_0.93-1 vsn_3.30.0 > [37] XML_3.98-1.1 xtable_1.7-1 XVector_0.2.0 > [40] zlibbioc_1.8.0 >> > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor