[BioC] how deal with multiplicate affy probes?

[Johnnidis, Jonathan]

Hi Bioconductor,

I'm a new list member and am not quite sure if this question is appropriate for the list, but will shoot anyway. I'm analyzing a bunch of data from Affy MgU74Av2 chips and am a bit perplexed as to how to treat conflicting expression data from multiplicate probe sets (that is a gene that has  >1 probe set designed against it (for example, 97569_r_at and 97658_r_at are both probes for the Insulin gene). 

Specifically, if probe #1 for geneX indicates significant fold change for that gene, but probe #2 indicates something else (no fold change, or even fold change in the opposite direction! (rare, but possible)), how can the expression status of geneX be properly evaluated?  Can one probe's measurement be considered more reliable than another's (and thus toss the one you suspect is wrong (although this could introduce experimental bias))? Or is it most appropriate to average the signal values for multiplicate probes together? Or is there some other method?

On the MgU74Av2 chip at least, by my calculations there are at least 1079 genes that have >1 probe agianst them (2323 probes total that are 'multiplicates'), so the numbers are great enough to potentially impact my analysis.  Any ideas/suggestions/criticisms will be much appreciated.

with thanks,

Jonathan Johnnidis