[BioC] affy - pm() and mm() not returning affyids

Mark Larsen larsenmtl at comcast.net
Wed Jun 1 04:40:51 CEST 2005

In the vignette "Description of Affy" it is sometimes shown tht the pm() 
and mm() functions will return the affyIDs as row names while the sample 
names as column names.  When I execute this, though, using R 1.9.1 and 
affy 1.4.1 (I think), I just get a matrix with the sample names as 
column headers but no row.names.  Also, in the vignette, it states you 
can get the affyids using probeNames.  This works but the probeNames are 
not numbered as they are when returned (as it is shown then can be) 
using pm() or mm() (see page 14 of the vignette).

So my question is two fold (sorry for the long winded explanation).  How 
do I get mm() and pm() to return affyIDs with numbers OR can I take it 
for granted that the probeNames returned using probeNames are in order? 
  I need to map the affyID to a specific sequence (ie compare sequence 
to Raw Intensity) and they differ based on the number.


Mark Larsen

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