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SILAC statistics

Posted: Fri May 03, 2013 4:53 am
by gorlukatko
Hi,
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.
thank you
john