[BioC] Feature intensities in affy data

Rafael A. Irizarry ririzarr at jhsph.edu
Sat Apr 26 12:29:36 MEST 2003


once you use expresso you have an exprSet not an AffyBatch. you have
expression measures not probe level data... so no pms nor mms.

On Fri, 25 Apr 2003, Crispin Miller wrote:

> 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 at jhsph.edu]
> > Sent: 24 April 2003 23:59
> > To: Eric
> > Cc: bioconductor at 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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> > >       Today's Topics:
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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 at lrz.tu-muenchen.de>
> > >       Subject: [BioC] too many cel files for RMA
> > >       To: <bioconductor at stat.math.ethz.ch>
> > >       Message-ID: <001e01c30a41$06545d10$6db2278d at 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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