Question: RE : Error in intgroup of arrayQualityMetrics package
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7.4 years ago by
Guest User12k
Guest User12k wrote:
I am using arraQualityMetrics package installed from Bioconductor site and R version that I am using is 2.15.0 The input for the function was eset and for the intgroup argument character vector "Tissue". There is a column named Tissue in my phenoData of the eset. But it still gives me an error saying the elements of intgroup do not match the column names of the pData(eset). I don't know what wrong I am doing. The error look like this : Error in prepData(expressionset,intgroup=intgroup): all elements of 'intgroup' should match column names of pData(expressionset) -- output of sessionInfo(): > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-redhat-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=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.4.6 arrayQualityMetrics_3.12.0 [3] affy_1.34.0 limma_3.12.1 [5] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 affyPLM_1.32.0 annotate_1.34.0 [4] AnnotationDbi_1.18.1 beadarray_2.6.0 BeadDataPackR_1.8.0 [7] Biostrings_2.24.1 Cairo_1.5-1 cluster_1.14.2 [10] colorspace_1.1-1 DBI_0.2-5 genefilter_1.38.0 [13] grid_2.15.0 Hmisc_3.9-3 hwriter_1.3 [16] IRanges_1.14.3 lattice_0.20-6 latticeExtra_0.6-19 [19] plyr_1.7.1 preprocessCore_1.18.0 RColorBrewer_1.0-5 [22] reshape2_1.2.1 RSQLite_0.11.1 setRNG_2011.11-2 [25] splines_2.15.0 stats4_2.15.0 stringr_0.6 [28] survival_2.36-12 SVGAnnotation_0.9-0 tools_2.15.0 [31] vsn_3.24.0 XML_3.9-4 xtable_1.7-0 [34] zlibbioc_1.2.0 > intgroup [1] "Tissue" > str(intgroup) chr "Tissue" Sorry I wont be able to provide you with the detailed information of the pData. But the colnames(pData(eset)) has one of columns named as "Tissue" and the class of the this column is factor. Thank you. -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 7.3 years ago by Tim Rayner270 • written 7.4 years ago by Guest User12k
Answer: RE : Error in intgroup of arrayQualityMetrics package
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gravatar for Wolfgang Huber
7.3 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Sonal, you asked the same question before: https://stat.ethz.ch/pipermail/bioconductor/2012-June/045922.html and I replied, asking you for more information that is needed to diagnose your problem. Now, you post this again, adding that you won't be able to provide the needed information. Sorry, but this means I am not able to provide help. The 'intgroup'-related functionality in the package works, as is shown for several examples in the package vignette. best wishes Wolfgang Sonal Bakiwala [guest] scripsit 06/15/2012 08:30 AM: > > I am using arraQualityMetrics package installed from Bioconductor site and R version that I am using is 2.15.0 > > The input for the function was eset and for the intgroup argument character vector "Tissue". There is a > column named Tissue in my phenoData of the eset. > > But it still gives me an error saying the elements of intgroup do not match the column names of the pData(eset). > I don't know what wrong I am doing. > > The error look like this : > > Error in prepData(expressionset,intgroup=intgroup): > all elements of 'intgroup' should match column names of pData(expressionset) > > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-redhat-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=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.4.6 arrayQualityMetrics_3.12.0 > [3] affy_1.34.0 limma_3.12.1 > [5] Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 affyPLM_1.32.0 annotate_1.34.0 > [4] AnnotationDbi_1.18.1 beadarray_2.6.0 BeadDataPackR_1.8.0 > [7] Biostrings_2.24.1 Cairo_1.5-1 cluster_1.14.2 > [10] colorspace_1.1-1 DBI_0.2-5 genefilter_1.38.0 > [13] grid_2.15.0 Hmisc_3.9-3 hwriter_1.3 > [16] IRanges_1.14.3 lattice_0.20-6 latticeExtra_0.6-19 > [19] plyr_1.7.1 preprocessCore_1.18.0 RColorBrewer_1.0-5 > [22] reshape2_1.2.1 RSQLite_0.11.1 setRNG_2011.11-2 > [25] splines_2.15.0 stats4_2.15.0 stringr_0.6 > [28] survival_2.36-12 SVGAnnotation_0.9-0 tools_2.15.0 > [31] vsn_3.24.0 XML_3.9-4 xtable_1.7-0 > [34] zlibbioc_1.2.0 >> intgroup > [1] "Tissue" >> str(intgroup) > chr "Tissue" > > Sorry I wont be able to provide you with the detailed information of the pData. > But the colnames(pData(eset)) has one of columns named as "Tissue" and the class of the this column is factor. > > Thank you. > > -- > 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 7.3 years ago by Wolfgang Huber13k
Answer: RE : Error in intgroup of arrayQualityMetrics package
0
gravatar for Tim Rayner
7.3 years ago by
Tim Rayner270
Tim Rayner270 wrote:
Hi Sonal, You could try rearranging pData(eset) so that the "Tissue" column is the first column, or within the first few columns. There's some preprocessing code in the arrayQualityMetrics:::cleanUpPhenoData function which limits the number of columns which will be carried forward into the QC (maxcol=10). Also, the contents of the "Tissue" column must not be either all the same or all different (a quite reasonable requirement). Cheers, Tim -- Tim Rayner Bioinformatician Smith Lab, CIMR University of Cambridge On 15 June 2012 07:30, Sonal Bakiwala [guest] <guest at="" bioconductor.org=""> wrote: > > I am using arraQualityMetrics package installed from Bioconductor site and R version that I am using is 2.15.0 > > The input for the function was eset and for the intgroup argument character vector "Tissue". There is a > column named Tissue in my phenoData of the eset. > > But it still gives me an error saying the elements of intgroup do not match the column names of the pData(eset). > I don't know what wrong I am doing. > > The error look like this : > > Error in prepData(expressionset,intgroup=intgroup): > all elements of 'intgroup' should match column names of pData(expressionset) > > > > ?-- output of sessionInfo(): > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-redhat-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=C ? ? ? ? ? ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] BiocInstaller_1.4.6 ? ? ? ?arrayQualityMetrics_3.12.0 > [3] affy_1.34.0 ? ? ? ? ? ? ? ?limma_3.12.1 > [5] Biobase_2.16.0 ? ? ? ? ? ? BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > ?[1] affyio_1.24.0 ? ? ? ? affyPLM_1.32.0 ? ? ? ?annotate_1.34.0 > ?[4] AnnotationDbi_1.18.1 ?beadarray_2.6.0 ? ? ? BeadDataPackR_1.8.0 > ?[7] Biostrings_2.24.1 ? ? Cairo_1.5-1 ? ? ? ? ? cluster_1.14.2 > [10] colorspace_1.1-1 ? ? ?DBI_0.2-5 ? ? ? ? ? ? genefilter_1.38.0 > [13] grid_2.15.0 ? ? ? ? ? Hmisc_3.9-3 ? ? ? ? ? hwriter_1.3 > [16] IRanges_1.14.3 ? ? ? ?lattice_0.20-6 ? ? ? ?latticeExtra_0.6-19 > [19] plyr_1.7.1 ? ? ? ? ? ?preprocessCore_1.18.0 RColorBrewer_1.0-5 > [22] reshape2_1.2.1 ? ? ? ?RSQLite_0.11.1 ? ? ? ?setRNG_2011.11-2 > [25] splines_2.15.0 ? ? ? ?stats4_2.15.0 ? ? ? ? stringr_0.6 > [28] survival_2.36-12 ? ? ?SVGAnnotation_0.9-0 ? tools_2.15.0 > [31] vsn_3.24.0 ? ? ? ? ? ?XML_3.9-4 ? ? ? ? ? ? xtable_1.7-0 > [34] zlibbioc_1.2.0 >> intgroup > [1] "Tissue" >> str(intgroup) > ?chr "Tissue" > > Sorry I wont be able to provide you with the detailed information of the pData. > But the colnames(pData(eset)) has one of columns named as "Tissue" and the class of the this column is factor. > > Thank you. > > -- > 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
ADD COMMENTlink written 7.3 years ago by Tim Rayner270
Dear Tim thanks for spotting this. That's indeed an unintended interaction of this cleanUpPhenoData function (which we needed after seeing some highly verbose and redundant ExpressionSet objects generated from ArrayExpress) and the 'intgroup' functionality. As a workaround, what you suggest below is perfect. Fixing this, as well as the suggestions by Daniel Aaen Hansen of 1 June, are on the to-do list for this summer. best wishes Wolfgang Jun/18/12 2:01 PM, Tim Rayner scripsit:: > Hi Sonal, > > You could try rearranging pData(eset) so that the "Tissue" column is > the first column, or within the first few columns. There's some > preprocessing code in the arrayQualityMetrics:::cleanUpPhenoData > function which limits the number of columns which will be carried > forward into the QC (maxcol=10). Also, the contents of the "Tissue" > column must not be either all the same or all different (a quite > reasonable requirement). > > Cheers, > > Tim > > > -- > Tim Rayner > Bioinformatician > Smith Lab, CIMR > University of Cambridge > > > On 15 June 2012 07:30, Sonal Bakiwala [guest] <guest at="" bioconductor.org=""> wrote: >> >> I am using arraQualityMetrics package installed from Bioconductor site and R version that I am using is 2.15.0 >> >> The input for the function was eset and for the intgroup argument character vector "Tissue". There is a >> column named Tissue in my phenoData of the eset. >> >> But it still gives me an error saying the elements of intgroup do not match the column names of the pData(eset). >> I don't know what wrong I am doing. >> >> The error look like this : >> >> Error in prepData(expressionset,intgroup=intgroup): >> all elements of 'intgroup' should match column names of pData(expressionset) >> >> >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-redhat-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=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.4.6 arrayQualityMetrics_3.12.0 >> [3] affy_1.34.0 limma_3.12.1 >> [5] Biobase_2.16.0 BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.24.0 affyPLM_1.32.0 annotate_1.34.0 >> [4] AnnotationDbi_1.18.1 beadarray_2.6.0 BeadDataPackR_1.8.0 >> [7] Biostrings_2.24.1 Cairo_1.5-1 cluster_1.14.2 >> [10] colorspace_1.1-1 DBI_0.2-5 genefilter_1.38.0 >> [13] grid_2.15.0 Hmisc_3.9-3 hwriter_1.3 >> [16] IRanges_1.14.3 lattice_0.20-6 latticeExtra_0.6-19 >> [19] plyr_1.7.1 preprocessCore_1.18.0 RColorBrewer_1.0-5 >> [22] reshape2_1.2.1 RSQLite_0.11.1 setRNG_2011.11-2 >> [25] splines_2.15.0 stats4_2.15.0 stringr_0.6 >> [28] survival_2.36-12 SVGAnnotation_0.9-0 tools_2.15.0 >> [31] vsn_3.24.0 XML_3.9-4 xtable_1.7-0 >> [34] zlibbioc_1.2.0 >>> intgroup >> [1] "Tissue" >>> str(intgroup) >> chr "Tissue" >> >> Sorry I wont be able to provide you with the detailed information of the pData. >> But the colnames(pData(eset)) has one of columns named as "Tissue" and the class of the this column is factor. >> >> Thank you. >> >> -- >> 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 > > _______________________________________________ > 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 > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD REPLYlink written 7.3 years ago by Wolfgang Huber13k
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