[BioC] affy - pm() and mm() not returning affyids
larsenmtl at comcast.net
larsenmtl at comcast.net
Wed Jun 1 16:09:58 CEST 2005
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.
> 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
> > pm(affybatch.example, gn)
> 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.
> 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.
> Mark Larsen
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