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Hi Ankhee, On Aug 6, 2009, at 1:01 AM, ankhee dutta wrote: > Hi all, > I am having problem in merging technical spot replicates in > microarray data > for further analysis of it. I want to get rid of outliers so i dont > want to > just average them. I have microarray datasets from different > experiments > with their log2 based ratio values and nothing else so how can i > detect the > outliers. > I tried to use tools like GEPAS but it was just averaging the > replicate > values.So please suggest some tools or ways to do this. > Please help me out. > Thank you in advance.Any relevant answer will be appreciated. Sorry, it's not clear to me if you're talking about summarizing replicate spots on one array, or across arrays -- either way, I believe the limma package should be able to help you out here. The package comes with a rather extensive user guide that wouldn't hurt to read through as it covers many aspects of dealing with microarray data in R. As an example, here's an older version of the doc which mentions duplicate spots on an array: http://pbil.univ- lyon1.fr/library/limma/doc/usersguide.html#DuplicateSpots Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact