[BioC] PLIER affinities redux

[Jeremy Gollub]

Hi, All -

James MacDonald (I think) answered my previous posting, and I promptly
lost the message.  Thanks, James, and apologies.

The issue at hand was strange and (I believe) incorrect reporting of
probe affinities from justPlier (plier package).  At James' suggestion
I have update to R 2.2.0 and plier 1.2.0, but the affinities are still
coming back in a sparse <# probe pairs> X <# arrays> matrix, rather than
as a useful vector.  The colnames of this matrix are the sampleNames from
the eset provided to justPlier; the rownames are the probeNames.

James, you said this doesn't happen to you.  How do you retrieve the
affinities?  Maybe I'm just looking at the wrong slot (see below).
Looking at the justPlier source code, though, I don't see any other
way to get them.

Also, does justPlier allow one to pass the affinities back to another
invocation of the method, rather than computing them from the current
data?

Thanks,

- Jeremy Gollub


The session (edited for readability):

# ---------------------------------------------------------------------

> sessionInfo())
R version 2.2.0, 2005-10-06, i386-pc-mingw32 

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"    
[7] "datasets"  "base"     

other attached packages:
rae230acdf      plier       affy    Biobase     qvalue 
  "1.10.0"    "1.2.0"    "1.8.1"    "1.8.0"    "1.4.0"

> data <- ReadAffy()
> data
AffyBatch object
size of arrays=602x602 features (50972 kb)
cdf=RAE230A (15923 affyids)
number of samples=18
number of genes=15923
annotation=rae230a

> res <- justPlier(data, get.affinities = TRUE)
> dim(res at description@preprocessing$affinity)
[1] 175477     18

> sum(res at description@preprocessing$affinity != 0)
[1] 175407

# ----------------------------------------------------------------------

-- 
Jeremy Gollub
jeremy at gollub.net