[BioC] removing SNP probes from Drosophila 2 microarray

[Eli Moss]

Hello all,

 I'm interested in finding probes with lower expression level due to a SNP mismatch and removing them, hopefully giving me a better measure of expression level even in those genes with sequences modified by a hybridization experiment.  I'm thinking of doing this by finding the changes between probe intensities between control and experimental arrays, which should be normally distributed, and removing all those probes outside some number of standard deviations from the mean.  My question is this: is there a package that does something like this, or do I need to write it myself?

Thank you,
Eli


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Eli Moss
Brown University, Computational Biology
+1 (413) 658-4227
Eli_Moss at Brown.edu