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Old 04-27-2014, 10:13 PM   #1
hyates
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Location: Kansas City

Join Date: Jan 2014
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Question Inquiry: p-values & q-values for cummeRbund volcano?

Hi,

Suppose I have the following command:
Code:
sigGene <- csVolcano(genes(cuffData), "A, "B")
It shows no differential expressed genes in the plot. It now can show some differential gene expression. Why? What changed? Is what being reported not taking into account the q-values which are adjusted?
Code:
sigGene <- csVolcano(genes(cuffData), "A, "B", alpha = 0.01, showSignificant =T)
Thanks,
GeekyOmega

PS - I looked at the bioconductor manual for cummeRbund. What is the default alpha for csVolcano()? Is it alpha = 0.05 for p-value/q-value? I can't figure out how it works exactly in the default/manual situation. Thanks.
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Old 07-08-2014, 06:18 AM   #2
sazz
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Hello Hyates,

Depending on the output, I can say alpha is for q-value. But in the volcano plot it is the corresponding p-value. If your cutoff for q-value is 0.01 you should see that red dots for p-value starts around -log(2.42) in volcano plot (it would be exactly at -2.00 if alpha was accounted for p-value).
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