[BioC] reading many affy U133 Plus_2.0

[Henrik Bengtsson]

Sure he can ;)  See the RmaPlm class. /Henrik


On 10/5/07, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> Yeah, but can he do fitPLM()? I was going to suggest that as well, but
> Henrik's page doesn't mention that as a possibility.
>
> Jim
>
>
>
> Mark Robinson wrote:
> > David,
> >
> > You might have a look at the R package 'aroma.affymetrix' ... you
> > should be able to read/process/analyze 100s of affy chips.  I
> > regularly process >50 exon arrays, which are far larger than U133s.
> > I believe you can do it all in less than 500M RAM.
> >
> > Full details are at:
> > http://groups.google.com/group/aroma-affymetrix
> >
> > Cheers,
> > Mark
> >
> >
> > On 05/10/2007, at 9:57 PM, <darteta001 at ikasle.ehu.es>
> > <darteta001 at ikasle.ehu.es> wrote:
> >
> >> Dear list,
> >>
> >> In order to normalise my data using fitPLM(), I need to create an
> >> affybatch using ReadAffy(). This time I think justRMA() is not an
> >> option I can use.
> >>
> >> Has anyone been successful at reading in a large group of Plus chips
> >> (say 100) using ReadAffy() and the normalise them using fitPLM() on
> >> a "normal" PC on Windows? What amount of memory is needed for it?
> >> Any examples on how many chips you might have loaded with memory
> >> details would be very appreciated.
> >>
> >> Regards,
> >>
> >> David
> >>
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> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
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>
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