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

Mark Dalphin mdalphin at amgen.com
Mon Dec 15 22:27:54 MET 2003


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 ...

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.


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)
One Amgen Center Drive                       +1-805-375-0680 (home)
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