Hi,
I had a similar problem - I couldn't get pm() and mm() to work after I
had uses expresso to do a mas5 normalisation on the data. I wonder if
this is the trouble?
Crispin
> -----Original Message-----
> From: Rafael A. Irizarry [mailto:ririzarr@jhsph.edu]
> Sent: 24 April 2003 23:59
> To: Eric
> Cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] Feature intensities in affy data
>
>
> you can get all the pms using the method pm. for example:
>
> Data <- ReadAffy()
> pms <- pm(Data)
>
> simliarly for mm
>
> mms <- mm(Data)
>
> the rownames of thes matrices will have the probe names followed by
a
> number telling you what probe it is in the ID.
>
> Names <- rownames(pms)
>
> you probably dont want the numbers so use:
>
> Names <- probeNames(Data)
>
> you can then create a data.frame combining these
>
> result <- data.frame(Names,pms,mms)
>
> this last one will be slow.
> and use the function wrtie.table to create a text file. look at the
> helpfile for this function as it has many options.
>
> hope this helps,
> rafael
>
>
>
> On Thu, 24 Apr 2003, Eric wrote:
>
> > Hi,
> >
> > In the affy package, is there a way to get all of the
> feature intensities
> > for the entire chip output as a text file along with
> columns defining
> > probe pair #, pm/mm, and AffyID? I'm just a biologist, so
> type slowly :)
> >
> > -E
> >
> > At 12:04 PM 4/24/2003 +0200, you wrote:
> >
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> > 1. too many cel files for RMA (J?rg Mages)
> >
> >
> >
>
----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 24 Apr 2003 11:08:08 +0200
> > From: J?rg Mages<mages@lrz.tu-muenchen.de>
> > Subject: [BioC] too many cel files for RMA
> > To: <bioconductor@stat.math.ethz.ch>
> > Message-ID: <001e01c30a41$06545d10$6db2278d@24affy>
> > Content-Type: text/plain
> >
> > Dear All,
> >
> > I do have a problem while reading in more than 20 cel files
> > using ReadAffy(). The error message is : can?t allocate
> > vector. Can anybody help?
> >
> > Thank?s in advance
> > Joerg
> >
> > [[alternate HTML version deleted]]
> >
> >
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> > End of Bioconductor Digest, Vol 2, Issue 26
> > *******************************************
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> > Eric Blalock, PhD
> > Dept Pharmacology, UKMC
> > 859 323-8033
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