[BioC] error with affycomp package
andrea.grilli at ior.it
andrea.grilli at ior.it
Fri Apr 20 12:49:49 CEST 2012
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
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