[BioC] problem in beadsummary vignette from beadarray

[Jenny Drnevich]

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