Hi,
Suppose I have the following command:
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?
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.
Suppose I have the following command:
Code:
sigGene <- csVolcano(genes(cuffData), "A, "B")
Code:
sigGene <- csVolcano(genes(cuffData), "A, "B", alpha = 0.01, showSignificant =T)
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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