[BioC] GCRMA Normalization Differences between Windows and MAC

[Wolfgang Huber]

Dear Martin

it would help if you were a bit more precise about how the results 
differ. Could you provide us a reproducible example (e.g. using the data 
in the ALLMLL package, 
http://www.bioconductor.org/packages/release/data/experiment instead of 
your own private files), code for a plot or other kind of comparison 
that shows what you perceive as an 'important difference', and also the 
output of sessionInfo()?

I doubt that the difference is related to "Windows" vs "Mac", but rather 
to changes in the "gcrma" package, and the package maintainer might have 
more insights on changes between the two versions (2.16 and 2.18.1), and 
where they are documented.

The svn log does report:
------------------------------------------------------------------------
r43600 | jmacdon | 2009-12-17 16:59:57 +0100 (gio, 17 dic 2009) | 1 line

Modifications to justGCRMA to keep consistent with gcrma. Because gcrma 
has become more complex (e.g., being able to use either the internal NSB 
estimates, MM probes, or NCprobes), it is no longer feasible to keep 
justGCRMA completely consistent. Instead, justGCRMA will only use the 
internal NSB estimates (which is the default for gcrma anyway).

	Best wishes
	Wolfgang

martin martinez ha scritto:
> 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.
> 
> Regards,
> 
>   Martín M.
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact