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

[larsenmtl at comcast.net]

Marcus,

Thanks,  I'm smacking myself in the forehead on that one....

I'll be working on upgrading soon.  In a corporate environment all software has to be re-validated with the new versions.  It makes for a headache.

Thanks again,

Mark


> 
> 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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