[BioC] problem in beadsummary vignette from beadarray
mer36 at cam.ac.uk
Thu Nov 13 20:56:15 CET 2008
Thanks for the note - it appears that the zip file on our website contains
a different dataFile to the one used to generate the vignette. I have
updated this now, so try downloading the file again. With the correct file,
you should be able to proceed without this warning.
>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.
> > library(beadarray)
>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
> > ?readBeadSummaryData
> > samples = as.factor(samples)
>Error in as.vector(x, mode) : invalid 'mode' argument
> > sessionInfo()
>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  RSQLite_0.7-1
>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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