[BioC] PLIER affinities redux

Matthew Hannah Hannah at mpimp-golm.mpg.de
Tue Oct 18 18:13:38 CEST 2005

I got distracted whilst still in draft and in the meantime Jim has responded. Anyway to add -

I pasted your code into my fresh BioC install and it doesn't work with the ATH1121501 array either, it's inherent in the justPlier code.
Looking at justPlier code shows that it returns a matrix of probeNames(eset) x sampleNames(eset) which is consistent with what we find. After investigating it seems the r$affinity (within justPlier) is 159683 values followed by zeros until length 1757546. This is ~100000 short of what is needed for 1 affinity per probepair but if you divide it by the number of arrays I had = 159683/7 = 22811.86 it is pretty close to the number of probesets on the array(22810). So this would imply a probesets x samples output matrix.

Not sure if this is still helpful after Jim's response.  


Dr. Matt Hannah
Max-Planck Institute of Molecular Plant Physiology
Am Mühlenburg 1
14476 Golm

+ 49 (331) 567 8255 (phone)
+ 49 (331) 567 8250 (fax)

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


- 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

> res <- justPlier(data, get.affinities = TRUE)
> dim(res at description <https://stat.ethz.ch/mailman/listinfo/bioconductor> @preprocessing$affinity)
[1] 175477     18

> sum(res at description <https://stat.ethz.ch/mailman/listinfo/bioconductor> @preprocessing$affinity != 0)
[1] 175407

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

Jeremy Gollub
jeremy at gollub.net <https://stat.ethz.ch/mailman/listinfo/bioconductor>

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