[BioC] screening for array outliers

Kimpel, Mark W mkimpel at iupui.edu
Mon Jul 12 18:46:54 CEST 2004

I am working with 2D gel electrophoresis proteomic datasets and would
like to develop or adapt a method for screening out entire gels, after
appropriate filtering out of artifacts, normalization, and imputation of
missing values, that are outliers. Each gel represents a sample from a
different animal and there are times when one animal in a group simply
doesn't respond the way others do. This will show up on clustering if
there is a clear difference between groups, where the outlier may
cluster with the experimental group or, in an extreme case, will form a
cluster of 1 all by itself.

I would like to approach this numerically and have looked at the Li/Wong
dChip approach implanted in BioC as fit.li.wong(affy) but am not sure
this model would be applicable for protein gels where there really are
no replicates within animal for each protein. On the other hand, perhaps
one could consider each set of gel spots as a probeset?

Any ideas would be greatly appreciated. Thanks,


Mark W. Kimpel MD

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