Dear all, I perfomred SAM analysis in my dataset and the sam.plot command that gave me estimates of the q-values for the significant genes. However all of those q-values were around 0.6. Does anyone know how these q-values are calculated? If the q-value is similar to p-value in interpretation, why these genes are significant? Should I take into account the q-values estimates for my analysis? What can I say? Thank in advance. Makis Motakis ---------------------- E Motakis, Mathematics E.Motakis@bristol.ac.uk

Hi Makis, the q-values are computed as described in John Storey's and Rob Tibshirani's paper "Statistical significance for genome-wide studies." HTH, Holger > Dear all, > > I perfomred SAM analysis in my dataset and the sam.plot command that gave > me estimates of the q-values for the significant genes. However all of > those q-values were around 0.6. > > Does anyone know how these q-values are calculated? > > If the q-value is similar to p-value in interpretation, why these genes > are > significant? > > Should I take into account the q-values estimates for my analysis? What > can > I say? > > Thank in advance. > Makis Motakis > > ---------------------- > E Motakis, Mathematics > E.Motakis@bristol.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > --