We are printing our own slides using the arabidopsis Operon oligo probe set- version3. There are about 5,000 duplicate genes (as represented by AGI numbers). Is there a script, in R perhaps, that can select duplicates prior to import in MapMan? Or does somebody have a mapping file for this probe set?

thanks,

Hi,

If you have duplicates it is definetely better to condense them to one item in MapMan, otherwise you see the same gene twice and this would also be not so nice for group-testing.
Bummer though, that not all genes are replicated, which would increase the power of testing....


But depending on your layout and statistical procedure that you are using, I could just provide you an R script. I have never worked with operon chips myself though.
You can contact me directly for that usadel AT mpimp-golm.mpg.de, because I would need some sample data. (I only use limma, which in my opinion is one of the best supported bioc packages)



Cheers,
Björn