[BioC] problem with function rma

[Steven McKinney]

>> 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

search() produces an email-proof list

> search()
 [1] ".GlobalEnv"        "package:Matrix"    "package:lattice"   "tools:RGUI"        "package:stats"     "package:graphics" 
 [7] "package:grDevices" "package:utils"     "package:datasets"  "package:methods"   "Autoloads"         "package:base"     

how about

> sessionInfo()

 [1] "rat2302cdf:1.14.0" "affyQCReport:1.12.0"

etc.


Steve McKinney


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Seth Falcon
Sent: Wed 5/30/2007 9:33 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] problem with function rma
 
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

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