[BioC] preprocessCore

[Martin Morgan]

Hi Irene --

irene.vicari at epfl.ch writes:

> Hello,
> I'm doing a project using Affymatrix but I have a problem. To use "RMA" I need
> to put in R:
> library(preprocessCore)
>
> but then when I put
> plac.rma <- rma(plac.new)
>
> R tells me
> Background correcting
> Normalizing
> Calculating Expression
> Errore in rma(plac.new) :
> function 'R_subColSummarize_medianpolish_log' not provided by package
> 'preprocessCore'

Your session info indicates that affyio is out-of-date compared to the
other packages. In a new R session, try

> source('http://bioconductor.org/biocLite.R')
> biocLite('affyio')

or, better, follow the instructions at

http://bioconductor.org/install

for updating all packages

> source("http://bioconductor.org/biocLite.R")
> update.packages(repos=biocinstallRepos(), ask=FALSE)

Martin

> What can I do? Do you have any idea what is the problem?
>
> I do not know if it can be useful if I give you
>
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=Italian_Switzerland.1252;LC_CTYPE=Italian_Switzerland.1252;LC_MONETARY=Italian_Switzerland.1252;LC_NUMERIC=C;LC_TIME=Italian_Switzerland.1252
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] hgu133acdf_2.3.0     geneplotter_1.20.0   annotate_1.20.0
>  [4] xtable_1.5-4         AnnotationDbi_1.4.0  lattice_0.17-15
>  [7] hgu95av2cdf_2.3.0    affydata_1.11.3      affyPLM_1.18.0
> [10] preprocessCore_1.4.0 gcrma_2.14.0         matchprobes_1.14.0
> [13] affy_1.20.0          Biobase_2.2.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.8.1       DBI_0.2-4          grid_2.8.0         KernSmooth_2.22-22
> [5] RColorBrewer_1.0-2 RSQLite_0.7-0
>
> Thanks a lot.
>
> Best regards,
> Irene Vicari
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793