q value in rna seq - (Sep/06/2013 )

What does q value in rna sequencing mean along with p value

The q-value is an adjusted p-value, taking in to account the false discovery rate (FDR).  Applying a FDR becomes necessary when we're measuring thousands of variables (e.g. gene expression levels) from a small sample set (e.g. a couple of individuals).  A p-value of 0.05 implies that we are willing to accept that 5% of all tests will be false positives.  An FDR-adjusted p-value (aka a q-value) of 0.05  implies that we are willing to accept that 5% of the tests found to be statistically significant (e.g. by p-value) will be false positives.  Such an adjustment is necessary when we're making multiple tests on the same sample.  See, for example, http://www.totallab.com/products/samespots/support/faq/pq-values.aspx.