Question: How to interpret gene-FDR plots
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gravatar for r.monil
3.9 years ago by
r.monil0
Canada
r.monil0 wrote:

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

cssam false discovery rate fdr • 1.6k views
ADD COMMENTlink modified 3.7 years ago by Irsan6.8k • written 3.9 years ago by r.monil0
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gravatar for Irsan
3.7 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

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.

ADD COMMENTlink written 3.7 years ago by Irsan6.8k
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