[BioC] error with affycomp package

[James W. MacDonald]

Hi Andrea,

On 4/20/2012 6:49 AM, andrea.grilli at ior.it wrote:
> 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?

I think you misunderstand the purpose of the affycomp package. This 
package isn't designed to work with your data, it is designed to work 
with the Affy and GeneLogic spike-in datasets. The goal of the package 
is to make it easy for people to compare their preferred summarization 
methods easily.

Best,

Jim

> 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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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099