Entering edit mode
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]]
