How to interpret gene-FDR plots

Question

[r.monil]

Hello everyone.

I am new to bioinformatics. I was wondering if someone could kindly explain to me how to interpret gene-FDR plots. I'm not sure if there's a formal term for these plots, but these are the ones that display the false discovery rate (y-axis) as a function of the number of genes called significant (x-axis). The reason why I'm asking about gene-FDR plots is because the main output of the csSAM package includes these plots. I have already read the paper (http://www.ncbi.nlm.nih.gov/pubmed/20208531) and done the tutorial related to the package but I cannot find an elaborate explanation of what the plots mean. All I know is that the FDR is the ratio of false positives (null hypotheses that were erroneously rejected) to all positives (null hypotheses that were rejected).

• Why is the FDR on the y-axis when it's the value that we control for?
• How do you interpret the 'slope' of the curve i.e. what does it mean when the curve looks like a line and when the curve is increasing?

Edit: For examples of these plots, see the third figure on this link http://www.ncbi.nlm.nih.gov/pubmed/20208531

Answer 1

[Irsan]

I think the third figure of the paper just shows an overview of how much genes are differentially between samples from individuals with acute rejection and stable post-transplant course. If the line does not cross y=0.05 there are no genes differentially expressed. This way you can quickly see that in monocytes there is the most sign of differential genes opposed to basophils.