Jeremy, 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. Cheers, Matt Dr. Matt Hannah Max-Planck Institute of Molecular Plant Physiology Am M?hlenburg 1 14476 Golm Germany + 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 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 <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="">