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Jeremy Gollub
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80
@jeremy-gollub-790
Last seen 10.2 years ago
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?
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
