[BioC] problem with function rma

[Seth Falcon]

Martin Morgan <mtmorgan at fhcrc.org> writes:
> R 2.5.0 is out, and so are the 1.14.x series of affy and Biobase. One
> thing that will change when you update is that affy will produce an
> eSet-based AffyBatch, which is slightly different:
>
> 1) update any old instances with  rat <- updateObject(RatData)
>
> 2) use read.AnnotatedDataFrame rather than read.phenoData.
>

Just to clarify: if you want to upgrade to the latest BioC packages,
you need to also upgrade to the latest release of R.

Based on your sessionInfo, it looks like you have a mix since you have
affy 1.14.0 (part of BioC 2.0 release) and your other packages are
part of the 1.9 release and appropriate for your version of R.

Did you install via some mechanism other than biocLite?  In any case,
mixing versions like this is not supported.  I would recommend
upgrading your R and reinstalling BioC using biocLite.

+ seth



>>> sessionInfo()
>> R version 2.4.0 (2006-10-03)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
>> [7] "utils"     "datasets"  "base"
>>
>> other attached packages:
>>   rat2302cdf affyQCReport   simpleaffy   genefilter     survival
>> affy
>>     "1.14.0"     "1.12.0"      "2.8.0"     "1.12.0"       "2.31"
>> "1.12.1"
>>       affyio      Biobase
>>      "1.2.0"     "1.12.2"
>>
>> Thanks a lot!
>> Juan
>>
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>
> -- 
> Martin Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
>
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-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org