[BioC] error with affycomp package

[andrea.grilli at ior.it]

Dear mailing list,
I'm trying to use affycomp package, but I'm confused on how to move to  
my CEL data files. I read the package documentation, did google  
search, and I also went into the "read.dilution/read.spikein"  
functions, understanding that there is some problem with the  
phenodata, but I cannot carry on to the next steps. Any suggestions?
Also one doubt, could the package be used also on HGU133 plus 2 platform?
Thanks,
Andrea


This is my script:
library("affy")
library("hgu133plus2.db")

Data = ReadAffy()	# import .CEL files
eset.rma <- rma(Data)
write.table(data.frame(exprs(eset.rma), check.names=FALSE),  
file="eset.rma.csv", sep=",", col.names=NA, quote=FALSE)		# save  
expression file

library("affycomp")
d <- read.spikein("eset.rma.csv", cdfName=c("hgu133a"), remove.xhyb=TRUE)

Error in `[.data.frame`(s, , sampleNames(pd)) :
   undefined columns selected

s <- read.newspikein("eset.rma.csv")

Error in `[.data.frame`(s, , sampleNames(pd)) :
   undefined columns selected



> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] tools     tcltk     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] hgu133plus2cdf_2.9.1  tkWidgets_1.32.0      DynDoc_1.32.0
  [4] widgetTools_1.32.0    hgu133plus2.db_2.6.3  org.Hs.eg.db_2.6.4
  [7] RSQLite_0.11.1        DBI_0.2-5             AnnotationDbi_1.16.19
[10] gcrma_2.26.0          affycomp_1.30.2       affy_1.32.1
[13] Biobase_2.14.0

loaded via a namespace (and not attached):
[1] affyio_1.22.0         BiocInstaller_1.2.1   Biostrings_2.22.0
[4] IRanges_1.12.6        preprocessCore_1.16.0 splines_2.14.2
[7] zlibbioc_1.0.1




Dr. Andrea Grilli
andrea.grilli at ior.it
phone 051/63.66.756

Laboratory of Experimental Oncology,
Development of  Biomolecular Therapies unit,
Rizzoli Orthopaedic Institute
Codivilla Putti Research Center
via di Barbiano 1/10
40136 - Bologna - Italy