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

w.huber at dkfz-heidelberg.de w.huber at dkfz-heidelberg.de
Mon Dec 15 23:56:53 MET 2003

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.

Best wishes

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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