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Old 03-04-2014, 03:01 PM   #1
Location: Milwaukee

Join Date: Dec 2011
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Default Are Cuffdiff q-values and p-values reliable when multiple treatments are analyzed?

Does anyone know if the q- and p-values output by CuffDiff are reliable when more than two treatments are compared in the the analysis.

Generating q-values for each gene in a two-treatment study is fairly strait forward. However, in a five-treatment study where each pair of treatments is compared, there are 15 pairwise comparisons for each gene. Can these comparisons be lumped together to generate the q-values, or should each pair of treatments be analyzed independently?
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Old 03-16-2014, 12:32 PM   #2
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Can anyone anwer this? Thank you
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cuffdiff, cufflinks, p-value, q-value, treatment

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