[BioC] GCRMA Normalization Differences between Windows and MAC

[Sean Davis]

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