I have executed cuffdiff for five different samples and got the FPKM values of genes across five different samples. Each sample contained a group of genes with very low FPKM values,representing low expression or background. I am planning to identify minimal expression value to avoid false positive estimation of gene expression. How can I identify the cut-off to avoid False- positive?
Can I identify by ploting density graph?
S1 S2 S3 S4 S5 1229.46 1.52844 0 10.7805 109.81 1229.96 814.614 2109.44 1138.93 673.454 1247.19 225.283 78.9963 76.2897 607.874 1250.08 3.94648 0.349388 11.9385 65.4146 1257.49 9.58456 8.32604 21273.9 8724.36
The above is the sample FPKM values for each stage. Can anyone please help me with this. Ive attached a plot which I copied from one research journal. How can get the similar plot for my data along with cutoff value