[BioC] PLIER affinities
James W. MacDonald
jmacdon at med.umich.edu
Mon Oct 17 14:52:32 CEST 2005
Jeremy Gollub wrote:
> Hi, All -
>
> I'm confused by the affinities returned by justPlier (from the plier
> package). My understanding is that the PLIER algorithm is supposed to
> produce a single affinity per PM/MM probe pair, across the entire set of
> arrays analyzed. However, justPlier() returns the values in a matrix of
> dimensions <# of probe pairs> X <# of chips> - e.g, 175,477 X 18, for
> 18 RAE230A arrays. The column names of this matrix are the names of the
> samples/arrays; the row names are the probe set names, repeated
> (apparently) once for each probe pair in the set (i.e., there are 11 rows
> with the name 1367452_at).
>
> Upon closer inspection, the matrix contains only 175,407 non-zero values,
> which would be consistent with a single value per probe pair. All columns
> contain some non-zero values, approximately 15,923 (one per probe set) in
> the first 11 columns, and 36 in the other 7 (perhaps due to control probe
> sets with more probes). All rows below 15,924 contain only zeros.
>
> Do I misunderstand? Or should the affinities in fact be a one-dimensional
> vector with one value per probe pair, making this an error in the way
> justPlier(), or the C++ code, return the values?
You are correct; justPlier should return only one value per probeset.
You might try upgrading to R-2.2.0 and BioC 1.7 - justPlier() works as
expected for me with the updated versions.
Best,
Jim
>
> SessionInfo() output below.
>
> Thanks,
>
> - Jeremy
>
>
>>sessionInfo()
>
> R version 2.1.1, 2005-06-20, i386-pc-mingw32
>
> attached base packages:
> [1]
> "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets"
> [8] "base"
>
> other attached packages:
> rae230acdf plier affy reposTools Biobase
> "1.5.1" "1.0.0" "1.6.7" "1.5.19" "1.5.12"
>
> --
> Jeremy Gollub, Ph.D.
> jgollub at genome.stanford.edu
>
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--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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