Hello list, I've been analyzing an experiment with two groups each with three replicates. My workflow was TopHat (paired end) -> Cufflinks -> CuffDiff. Unfortunately, there are not many significant differences identified by CuffDiff.
I am wondering whether one of my replicates might be an outlier. Does anybody have a suggestion on how to search for an outlier? The quality statistics of the unprocessed data looked equally good for all samples, so I don't think that this is a problem. Thanks, Dave
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