[BioC] Sheep samples measured with a Affymetrix bovine array

[Mattias Bair]

Hi all!

I'm currently facing a for me challenging job since I'm not an expert in microarray analysis and hope to get here some advice for my data analysis. I have to evaluate the data quality of sheep samples that have been measured on a Affymetrix bovine chip. Meaning, what are the over-/underexpressed genes from the sheep and how likely are those the right ones. Therefore, my first idea was to make a sequence match of the probe sequence or the gene associated to the probe on the sheep genome to get the gene of the sheep sticking to the probe. NCBI provides therefore the "cross-species megaBLAST" algorithm but it would be a daunting job. Is there a simple way to perform such an anlysis with bioconductor? Or is there a better way to get a result for my job?

Thanks.
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