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Old 03-15-2012, 05:13 PM   #3
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Location: Charlottesville, VA

Join Date: May 2011
Posts: 112

As for #3, using a different tool/algorithm to analyze your data isn't independent validation. There's a long discussion in other threads here on the relative merits of DESeq vs something like cufflinks. Some of the older posts are out of date - coming from a time before cufflinks allowed biological replicates.
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