[BioC] Problems with RMA in affy

[James W. MacDonald]

Hi Anupam,

anupam sinha wrote:
> Dear all,
>              I am trying to analyse a set of CEL files. But I am getting an
> error. Can anyone help me out with this? Thanks in advance.

Sure, just update your packages the correct way. You somehow have a 
mixture of really old affy and affyio packages with a nearly current 
Biobase, which would never happen if you had installed your bioconductor 
packages using biocLite().

The easiest for you would be to start a new R session, then

source("http://www.bioconductor.org/biocLite.R")
biocLite("Biobase")
library(Biobase)
z <- biocReposList()
update.packages(repos = z, ask = FALSE)

Best,

Jim


> 
> 
> 
> *> data<-ReadAffy()
>> data
> AffyBatch object
> size of arrays=1164x1164 features (10 kb)
> cdf=HG-U133_Plus_2 (54675 affyids)
> number of samples=12
> number of genes=54675
> annotation=hgu133plus2
> notes=
>> eset<-rma(data)
> Background correcting
> Normalizing
> Error in rma(data) :
>   VECTOR_ELT() can only be applied to a 'list', not a 'character'
> *
> *> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] cMAP_1.15.1          yeastExpData_0.9.9   graph_1.20.0
> [4] hgu133plus2cdf_2.4.0 affy_1.16.0          preprocessCore_1.6.0
> [7] affyio_1.6.1         Biobase_2.4.0
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.13 tools_2.9.0
> 
> 
> *Regards,
> 
> Anupam
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826