[BioC] GCRMA Normalization Differences between Windows and MAC
Wolfgang Huber
whuber at embl.de
Wed Mar 24 21:21:42 CET 2010
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
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