cummeRbund getSig(): alpha?

[cnyh]

I've used the following command to extract significant genes:

mySigGenes <- getSig(cuff, alpha = 0.05, level = "genes")

However, I don't understand why terms familiar to me such as "FPKM" and "q-value" are not arguments in this filtering process. Also, what does "alpha" mean?

[GenoMax]

P-value http://en.wikipedia.org/wiki/P-value.

[cnyh]

Ah, I see. So alpha is the cutoff for the p-value then. Does the same apply for q-value as well?