
Dear all,
 
I am working on plant biology and using Citrus array to identify DE genes in treated and untreated plants.
 
Citrus GeneChip (Affymetrix) is a mixture array:  2/3 of the contents are mRNA expression probe sets and 1/3 of them are TILLING derived from 165 kb genomic region.  My goal is to identify the DE genes in the TILLING region.  
 
I am planning to use LIMMA to get a set of significant DE genes. However I am not clear how to identify the DE genes in the TILLING region.  Any BioC package or other tools can do this job?
 
I greatly appreciate for any comment and advice.
 
Many Thanks,
 
Jason
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