[BioC] Error in readBeadSummaryData

[Jenny Drnevich]

Hi,

I found an error in the readBeadSummaryData function of beadarray. My 
code that worked in R 2.9.2 no longer works in R 2.11.1, and I also 
tried the code in the beadarrayUsersGuide(topic = "beadsummary") 
vignette. It also shows the same error (full code below): Error in 
grep(colnames(QC[[i]]), colnames(exprs(BSData)), extended = FALSE) : 
unused argument(s) (extended = FALSE). I looked through the code of 
readBeadSummaryData, and twice the grep() function with 
extended=FALSE is used. If I just remove the extended=FALSE, then it 
appears to work, but then I get a warning (code also below). I'll use 
my hack fix for now, and see if any problems come up with the column names.

Thanks,
Jenny


 > dataFile = "SampleProbeProfile.txt"
 > sampleSheet = "SampleSheet.csv"
 > qcFile = "ControlGeneProfile.txt"
 > BSData = readBeadSummaryData(dataFile = dataFile,
+ qcFile = qcFile, sampleSheet = sampleSheet,
+ controlID = "TargetID")
Error in grep(colnames(QC[[i]]), colnames(exprs(BSData)), extended = FALSE) :
   unused argument(s) (extended = FALSE)

#Read in a new function that's the same as readBeadSummaryData, but 
has the two instances
# extended=FALSE removed from grep() functions

 > source("C:/Downloads/BeadSummaryExample(3)/JDBead.R")
 > BSData = JDBead(dataFile = dataFile,
+     qcFile = qcFile, sampleSheet = sampleSheet,
+     controlID = "TargetID")
Warning messages:
1: In grep(colnames(QC[[i]]), colnames(exprs(BSData))) :
   argument 'pattern' has length > 1 and only the first element will be used
2: In grep(colnames(exprs(BSData)), samples) :
   argument 'pattern' has length > 1 and only the first element will be used
 >

 > sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
States.1252
[3] LC_MONETARY=English_United States.1252 
LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
  [1] splines   tcltk     grid      stats     graphics  grDevices 
datasets  utils     methods   base

other attached packages:
  [1] 
lumi_1.14.0           MASS_7.3-6            mgcv_1.6-2 
annotate_1.26.0
  [5] 
WGCNA_0.92            Hmisc_3.8-2           survival_2.35-8 
qvalue_1.22.0
  [9] 
flashClust_1.00       dynamicTreeCut_1.21   impute_1.22.0 
beadarray_1.16.0
[13] 
limma_3.4.4           affyQCReport_1.26.0   lattice_0.18-8 
xtable_1.5-6
[17] 
simpleaffy_2.24.0     genefilter_1.30.0     made4_1.22.0 
scatterplot3d_0.3-30
[21] 
gplots_2.8.0          caTools_1.10          bitops_1.0-4.1 
gdata_2.8.0
[25] 
gtools_2.6.2          RColorBrewer_1.0-2    ade4_1.4-14 
affyPLM_1.24.0
[29] preprocessCore_1.10.0 
gcrma_2.20.0          affycoretools_1.20.0  KEGG.db_2.4.1
[33] 
GO.db_2.4.1           RSQLite_0.9-1         DBI_0.2-5 
AnnotationDbi_1.10.1
[37] affy_1.26.1           Biobase_2.8.0         RWinEdt_1.8-2

loaded via a namespace (and not attached):
  [1] 
affyio_1.16.0      annaffy_1.20.0     biomaRt_2.4.0 
Biostrings_2.16.6  Category_2.14.0
  [6] 
cluster_1.12.3     GOstats_2.14.0     graph_1.26.0 
GSEABase_1.10.0    hwriter_1.2
[11] IRanges_1.6.8      Matrix_0.999375-39 
nlme_3.1-96        RBGL_1.24.0        RCurl_1.4-2
[16] tools_2.11.1       XML_3.1-0
 >


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