[BioC] arrayQualityMetrics - undefined columns selected

[Wolfgang Huber]

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="report1",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/arrayQualityMetrics/inst/doc/arrayQualityMetrics.pdf
> http://www.bioconductor.org/packages/2.12/bioc/html/arrayQualityMetrics.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
> 
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