What is the best Bioconductor package for processing and analyzing data from 4x44 drosophila agilent expression arrays?
Well the analysis of microarrays depends little on the platform. You will most likely be directed to Limma for differential gene expression analysis, but there are many more.
Microarrays do however differ in the steps needed to pre-process and normalise the data prior to downstream analysis. BioConductor has a specific package for 4x44 arrays. I don't know if there is an annotation package for the Drosophila arrays however.
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