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@hboi.fau.edu
Alt. Email: lisa.johnson.cohen@gmail.com

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