[BioC] problem with function rma

[Seth Falcon]

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
>>> 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"

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?

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org