[BioC] problem in beadsummary vignette from beadarray

[Matt Ritchie]

Dear Jenny,

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.

Best wishes,

Matt

>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.
>
>Thanks,
>Jenny
>
> > 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 :
>
>          backgroundCorrect,
>          imageplot,
>          plotMA
>
>
> > beadarrayUsersGuide(topic = "beadsummary")
>[1] "C:/PROGRA~1/R/R-28~1.0/library/beadarray/doc/beadsummary.pdf"
>
> > dataFile = "SampleProbeProfile.txt"
> > sampleSheet = "SampleSheet.csv"
> > qcFile = "ControlGeneProfile.txt"
> > BSData = readBeadSummaryData(dataFile = dataFile,
>+ qcFile = qcFile, sampleSheet = sampleSheet,
>+ controlID = "TargetID")
>Warning message:
>In readBeadSummaryData(dataFile = dataFile, qcFile = qcFile, 
>sampleSheet = sampleSheet,  :
>   Could not reconcile dataFile with sampleSheet information. 
>sampleSheet ignored.
>
> From section 4:
> > samples = pData(BSData.quantile)$Sample_Group
> > samples
>NULL
> > ?readBeadSummaryData
> > samples = as.factor(samples)
>Error in as.vector(x, mode) : invalid 'mode' argument
>
>
> > sessionInfo()
>R version 2.8.0 (2008-10-20)
>i386-pc-mingw32
>
>locale:
>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
>States.1252;LC_MONETARY=English_United 
>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>attached base packages:
>[1] tools     stats     graphics  grDevices utils     datasets  methods
>[8] base
>
>other attached packages:
>  [1] beadarray_1.10.0    sma_0.5.15          hwriter_0.93
>  [4] geneplotter_1.20.0  annotate_1.20.1     xtable_1.5-4
>  [7] AnnotationDbi_1.4.1 lattice_0.17-15     Biobase_2.2.1
>[10] limma_2.16.3
>
> loaded via a namespace (and not attached): [1] DBI_0.2-4 grid_2.8.0 
> KernSmooth_2.22-22 RColorBrewer_1.0-2 [5] 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
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at illinois.edu