[BioC] problem in beadsummary vignette from beadarray
drnevich at illinois.edu
Thu Nov 13 16:22:24 CET 2008
Hi Mark and others,
I was trying to get familiar with the beadarray package, and I was
going through the beadsummary topic vignette:
beadarrayUsersGuide(topic = "beadsummary") . I downloaded the
example data as indicated in the vignette, and unzipped them into my
working directory. However, I get a warning when reading in the data
that it could not reconcile the dataFile with the sampleSheet
information (full code and sessionInfo() below). This isn't a problem
for much of the vignette, but the code for section 4 Differential
Expression no longer works. I looked at the SampleSheet.csv file and
compared the Sentrix_ID names to those in the columns in
SampleProbeProfile.txt and they look the same, so I'm not sure why
the code is no longer working.
Loading required package: limma
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: hwriter
Loading required package: sma
Attaching package: 'beadarray'
The following object(s) are masked from package:limma :
> beadarrayUsersGuide(topic = "beadsummary")
> dataFile = "SampleProbeProfile.txt"
> sampleSheet = "SampleSheet.csv"
> qcFile = "ControlGeneProfile.txt"
> BSData = readBeadSummaryData(dataFile = dataFile,
+ qcFile = qcFile, sampleSheet = sampleSheet,
+ controlID = "TargetID")
In readBeadSummaryData(dataFile = dataFile, qcFile = qcFile,
sampleSheet = sampleSheet, :
Could not reconcile dataFile with sampleSheet information.
From section 4:
> samples = pData(BSData.quantile)$Sample_Group
> samples = as.factor(samples)
Error in as.vector(x, mode) : invalid 'mode' argument
R version 2.8.0 (2008-10-20)
attached base packages:
 tools stats graphics grDevices utils datasets methods
other attached packages:
 beadarray_1.10.0 sma_0.5.15 hwriter_0.93
 geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4
 AnnotationDbi_1.4.1 lattice_0.17-15 Biobase_2.2.1
loaded via a namespace (and not attached):
 DBI_0.2-4 grid_2.8.0 KernSmooth_2.22-22 RColorBrewer_1.0-2
Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at illinois.edu
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