I recently used the Tuxedo package to analyze RNA-seq data of four conditions each with four biological replicates. The Cuffdiff output .diff files indicate I have >2000 significantly differentially regulated genes. When I try to make a volcano plot using all the defaults in cummeRbund, there are only a few significant (red) points way up at the top of the figure (-log10(p value) >15). If I specifically add alpha=0.05, which is supposed to be the default, there are no longer significant points. Similarly in the scatterplot, if I use the colorByStatus = TRUE option, none of the points are colored. Does anyone have any suggestions?
Thanks so much,