[BioC] problem with function rma

James W. MacDonald jmacdon at med.umich.edu
Wed May 30 23:11:11 CEST 2007

Seth Falcon wrote:
> Seth Falcon <sfalcon at fhcrc.org> writes:
>>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.
> My comment here is bogus; I completely misread the sessionInfo
> output.  Sorry about that.
>>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.
> I still recommend upgrading :-)
>>>>other attached packages:
>>>>  rat2302cdf affyQCReport   simpleaffy   genefilter     survival
>>>>    "1.14.0"     "1.12.0"      "2.8.0"     "1.12.0"       "2.31"
>>>>      affyio      Biobase
>>>>     "1.2.0"     "1.12.2"
> Anyone have a suggestion of how R could format the sessionInfo output
> so that when it is cut/pasted into an email message it is readable?


Works for Thunderbird at least.



> + seth

James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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