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

[Marcus Davy]

It would probably be a good idea to obtain a newer version of R (2.1.0) and the Bioconductor affy package, and all its dependencies.

At the top of page 13/14 (v1.5.8-1 / v1.6.7) in the affy vignette, the following code,

> pm(affybatch.example, gn[100])
20A 20B 10A
D78156_at1 223.3 148.0 203.0
D78156_at2 149.8 155.5 131.0
D78156_at3 147.3 133.8 145.0
D78156_at4 162.3 131.8 134.0
D78156_at5 459.3 451.0 345.0
D78156_at6 711.0 526.8 601.8
D78156_at7 158.8 142.8 109.0
D78156_at8 219.0 211.3 167.0
D78156_at9 196.0 251.0 182.3
D78156_at10 1715.0 1291.8 1341.3
D78156_at11 710.5 506.3 553.0
D78156_at12 438.0 346.0 282.8
D78156_at13 439.0 311.3 387.0
D78156_at14 114.8 78.0 101.5
D78156_at15 114.0 87.0 89.5
D78156_at16 181.0 122.0 160.0

should give you the output you require, i.e. specifying a vector of affy ids as arguements to pm and mm adds row.names for the individual probes. 

Marcus

p.s. packageDescription("affy", field="Version") gives you your version of the affy package, 'version' describes your R install.


>>> Mark Larsen <larsenmtl at comcast.net> 1/06/2005 4:40:51 a.m. >>>
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.

Thanks,

Mark Larsen

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