[BioC] Problems with RMA in affy

[Martin Morgan]

Hi Anupam --

Your packages are out of date. Follow the instructions at

  http://bioconductor.org/docs/install/

to update.

Martin

anupam sinha <anupam.contact at gmail.com> writes:

> 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.
>
>
>
> *> 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
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793