I am plotting my CuffDiff results in a scatter plot using CummeRbund. Without log10 transformation on FPKM values axes range up to 10000, but when applying log10 transformation on FPKM values, axes still range to 1000 - which seems to be too high?! Even 10 seems fairly high....What could be the problem here?
Another thing, when plotting a volcano plot there are o significant genes (red), although some of the not-significant genes (black) match the criteria of significance (p<0.05, log2(fold-change) -1/1). Any ideas?
Thank you so far!