[BioC] Feature intensities in affy data

[Rafael A. Irizarry]

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)
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>       ----------------------------------------------------------------------
> 
>       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
> 
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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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