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Old 06-11-2015, 10:04 PM   #1
mfahim
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Location: Pakistan

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Default Problems with q-value in RNAseq

I have four subjects (one wildtype and three mutants, no replications) at two different conditions (a total of 8 samples).. cuffdiff tells me there is no significant difference based on adjusted p-value (aka q-value).

This is why I guess q-value is just overrated.. and is not applicable to every RNAseq analysis.

What do you say?. I have attached expression bar plot to this post and would appreciate your comments on statistics.
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Old 06-11-2015, 11:06 PM   #2
dpryan
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Default

FYI, an adjusted p-value and a q-value aren't actually the same thing, though they're related.

I have no clue how you came to the conclusion that this somehow indicates that adjusted p-values are overrated. This is a good example of how high variance in an under-powered experiment leads to insignificant results. Adjusted p-values have nothing to do with that.

Compensating for multiple corrections is applicable to EVERY RNAseq analysis like yours.
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Old 06-12-2015, 12:40 AM   #3
mfahim
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Default I got an excellent explanation to my querry..

https://www.biostars.org/p/146223/#146242
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