[BioC] PLIER affinities redux

[James W. MacDonald]

Hi Jeremy,

Seems I misunderstood your earlier email. I somehow thought you were 
talking about expression values, not the affinities. I get the same sort 
of result for the affinities that you are reporting.

However it doesn't appear to be a sparse matrix per se, but a matrix 
with a bunch of zeros padded on the end.

 > pset <- justPlier(dat, get.affinities = TRUE)
 > pset
Expression Set (exprSet) with
         54675 genes
         10 samples
                  phenoData object with 1 variables and 10 cases
          varLabels
                 sample: arbitrary numbering
 > dim(pset at description@preprocessing$affinity)
[1] 604258     10
 > sum(rowSums(pset at description@preprocessing$affinity) != 0)
[1] 54676
 > a <- which(rowSums(pset at description@preprocessing$affinity) != 0)
 > range(a)
[1]     1 54676

This is what I get with a HG-U133Plus_2 chip. It looks to me like there 
are indeed affinities for each probeset (rather than each probe), but 
the vector of affinities that is output by the C++ code is padded with a 
bunch of zeros. Maybe the result is different for other chips?

Anyway, this is probably a question for Crispin Miller, who maintains 
the package.

Best,

Jim



Jeremy Gollub wrote:
> 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
> 
> # ----------------------------------------------------------------------
> 


-- 
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