Question: arrayQualityMetrics - undefined columns selected
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gravatar for Lisa Cohen
5.8 years ago by
Lisa Cohen50
United States
Lisa Cohen50 wrote:
Hi, I'm trying to find the best way to do a quality assessment of a microarray data set. I made the ExpressionSet from scratch (output below), since data were collected with a custom Agilent microarray. Using the most updated version of the arrayQualityMetrics package (downloaded yesterday, 16 October 2013), it gives the error "undefined columns selected" (output below). What does that mean? I'm confused about what columns the function is trying to select. Thank you in advance! >arrayQualityMetrics(expressionset=sponge_ExpressionSet,outdir="report 1",force=TRUE,intgroup=c("Chip Number","Hyb Date"))The report will be written into directory 'report1'. Error in `[.data.frame`(x, order(x, na.last = na.last, decreasing = decreasing)) : undefined columns selectedIn addition: Warning messages:1: In maximumLevels(fac, n = length(colors)) : A factor was provided with 9 levels, but only the first 9 were used for coloring.2: In maximumLevels(fac, n = length(colors)) : A factor was provided with 9 levels, but only the first 9 were used for coloring.3: In maximumLevels(fac, n = length(colors)) : A factor was provided with 9 levels, but only the first 8 were used for coloring. >sponge_ExpressionSetExpressionSet (storageMode: lockedEnvironment) assayData: 15744 features, 72 samples element names: exprs protocolData: none phenoData sampleNames: 1_1 1_2 ... 9_8 (72 total) varLabels: Chip Number File Name ... Name (9 total) varMetadata: labelDescription featureData featureNames: 1 2 ... 15744 (15744 total) fvarLabels: Column Row ... X.1 (23 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: >sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoData =pd,experimentData=experimentData,featureData=an) http://www.bioconductor.org/packages/2.12/bioc/vignettes/arrayQualityM etrics/inst/doc/arrayQualityMetrics.pdf http://www.bioconductor.org/packages/2.12/bioc/html/arrayQualityMetric s.html Thank you! Lisa --- Lisa Cohen, M.Sc. Marine Ecosystem Health, Harbor Branch Oceanographic Institute at Florida Atlantic University 5600 N. US Hwy 1 Fort Pierce, FL 34946 Phone: (772) 242-2396 Fax: (772) 468-0757 Email:lcohen49@hboi.fau.edu Alt. Email: lisa.johnson.cohen@gmail.com [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.8 years ago by Wolfgang Huber13k • written 5.8 years ago by Lisa Cohen50
Answer: arrayQualityMetrics - undefined columns selected
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gravatar for Wolfgang Huber
5.8 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Lisa Thank you for the report. Can you make available to me (possibly off-list) the object 'sponge_ExpressionSet' needed to reproduce and investigate the error? Kind regards Wolfgang Il giorno Oct 17, 2013, alle ore 10:04 pm, Lisa Cohen <lisa.johnson.cohen at="" gmail.com=""> ha scritto: > Hi, I'm trying to find the best way to do a quality assessment of a > microarray data set. I made the ExpressionSet from scratch (output below), > since data were collected with a custom Agilent microarray. Using the most > updated version of the arrayQualityMetrics package (downloaded yesterday, > 16 October 2013), it gives the error "undefined columns selected" (output > below). What does that mean? I'm confused about what columns the function > is trying to select. Thank you in advance! > > >> arrayQualityMetrics(expressionset=sponge_ExpressionSet,outdir="repo rt1",force=TRUE,intgroup=c("Chip Number","Hyb Date"))The report will be written into directory 'report1'. Error in `[.data.frame`(x, order(x, na.last = na.last, decreasing = decreasing)) : > undefined columns selectedIn addition: Warning messages:1: In > maximumLevels(fac, n = length(colors)) : > A factor was provided with 9 levels, but only the first 9 were used > for coloring.2: In maximumLevels(fac, n = length(colors)) : > A factor was provided with 9 levels, but only the first 9 were used > for coloring.3: In maximumLevels(fac, n = length(colors)) : > A factor was provided with 9 levels, but only the first 8 were used > for coloring. > >> sponge_ExpressionSetExpressionSet (storageMode: lockedEnvironment) > assayData: 15744 features, 72 samples > element names: exprs > protocolData: none > phenoData > sampleNames: 1_1 1_2 ... 9_8 (72 total) > varLabels: Chip Number File Name ... Name (9 total) > varMetadata: labelDescription > featureData > featureNames: 1 2 ... 15744 (15744 total) > fvarLabels: Column Row ... X.1 (23 total) > fvarMetadata: labelDescription > experimentData: use 'experimentData(object)' > Annotation: > >> sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoDa ta=pd,experimentData=experimentData,featureData=an) > > > > http://www.bioconductor.org/packages/2.12/bioc/vignettes/arrayQualit yMetrics/inst/doc/arrayQualityMetrics.pdf > http://www.bioconductor.org/packages/2.12/bioc/html/arrayQualityMetr ics.html > > Thank you! > > Lisa > > --- > Lisa Cohen, M.Sc. > Marine Ecosystem Health, > Harbor Branch Oceanographic Institute > at Florida Atlantic University > 5600 N. US Hwy 1 > Fort Pierce, FL 34946 > Phone: (772) 242-2396 > Fax: (772) 468-0757 > Email:lcohen49 at hboi.fau.edu > Alt. Email: lisa.johnson.cohen at gmail.com > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 5.8 years ago by Wolfgang Huber13k
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