We started to do SILACs recently. I would like to analyze the resulting low/heavy ratio lists by some better method than just a simple FC. Is there some (free) software that implements some statistical methods for detection of proteins with changed low/heavy ratio? What is a proper handling of datasets where you have low/heavy and heavy/low replicates.
Search algorithms, post-searching processing, quantitation software, etc. Share and discuss software here.
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