[BioC] GCRMA Normalization Differences between Windows and MAC

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Tue Mar 23 15:18:37 CET 2010

I am not following gcrma very closely, but this exact question seems
like a question that has been discussed in at least 5 lengthy threads
over the last year or so.  So I would strongly advise spending time
looking at the email archives.


On Tue, Mar 23, 2010 at 8:55 AM, Sean Davis <seandavi at gmail.com> wrote:
> On Tue, Mar 23, 2010 at 8:46 AM, martin martinez
> <tininmartinez at gmail.com> wrote:
>> I am performing a gene expression analysis and I founded important
>> differences between the results of the GCRMA normalization obtained in a
>> Windows machine (gcrma ver.2.16) and a MAC one (gcrma ver.2.18.1). It
>> consists in a cut off, so all the lower values dissapear. The code is next:
>> library(affy)
>> library(gcrma)
>> affy.data= ReadAffy()
>> eset.gcrma=justGCRMA() (the same as eset.gcrmax=gcrma(affy.data))
>> my question is about default values. Does them variate between versions? The
>> difference is very significant and I tried changing all the arguments, but
>> not satisfactory results are obtained.
> Hi, Martin.
> It is quite possible that there are changes between versions of code
> that might be expected to change results.  You'll want to use the same
> versions in order to make a valid comparison.  If you do find
> differences when using the same versions, you'll probably need to
> provide a reproducible example and sessionInfo() for both platforms.
> Sean
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