[BioC] Methods to access GeneName to ProbeID in package Affy

[w.huber at dkfz-heidelberg.de]

Hi Mark,

this is documented in the vignette to the affy package, section 7.
To repeat it here, you can get the probe set names by

   psets = ls(hgu95av2cdf)

(replace "hgu95av" by whatever your chip name is). The indices of
the j-th probe set's PM and MM probes by

  get(psets[j], hgu95av2cdf)

and use these to subset the exprs matrix of the AffyBatch object.

Alternatively, a dataframe that maps probe Ids and probe set Ids (and
provides the sequence as well) is available in the probe packages, e.g.
hgu95av2probe.

Best wishes
 Wolfgang

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber
-------------------------------------

On Mon, 15 Dec 2003, Mark Dalphin wrote:

> Hi,
>
> I'm trying to extract information from an AffyBatch object. I want to prepare
> a table which contains:
>
> AffyID	ProbeID	PM-1	PM-2	PM-3 ...
>
> Where:
> AffyID is also called the GeneName.
> ProbeID is the ID for the specific reporter on the chip.
> PM-1, PM-2, ... are the PerfectMatch intensities for several different chips
> which are part of the the expression set.
>
> I can see using the 'pm' method to extract most of this where the ProbeID and
> PM-1 will be row- and col-names in a matrix (this is great), but then I don't
> see how to associate the Affy-ID with ProbeID anywhere. A two-column data
> frame would be just fine.
>
> Any help would be appreciated.
>
> Thanks,
> Mark
>
> PS I am fairly familliar with R, but many of the data structures in
> BioConductor seem opaque to me. I believe this is due to the new S4 class
> structure being used, but I am not certain. Any pointers to how these data
> are represented and how to browse them would be appreciated; my old stand-by
> of str() is failing on these data:
>
> > str(spikein)
> List of 59
>  $ : int [1:59] 1 2 3 4 5 6 7 8 9 10 ...
>  $ :Error in .subset2(x, i) : subscript out of bounds
>
> R version 1.8.0 under RedHat Linux 7.3
>
> --
> Mark Dalphin                          email: mdalphin at amgen.com
> Mail Stop: 29-2-A                     phone: +1-805-447-4951 (work)
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>
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