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
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.
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