Odds ratio interpretation about enrichr_issues HOT 4 CLOSED

Will do. Thank you so much for the helpful feedback. It is much appreciated!

from enrichr_issues.

I have a question how to read the documentation of the odds ratio from the help page:

where: a are the overlapping genes, b are the genes in the annotated set - overlapping genes, c- are the genes in the input set - overlapping genes, and d- are the 20,000 genes (or total genes in the background) - genes in the annotated set - genes in the input set + overlapping genes

How should one read the pluses (+) and minus (-) in the text?

For example:

What is d?

• 20,000 genes (or no. of background genes) minus genes in the annotated set minus genes in the input minus genes overlapping?
• if that is true, then I would write minus and plus
• and remove the d- minus after d.

If it is a mix of minus (-) in the mathematical sense and hyphens, it needs some clarifications:) It's a great tool and the documentation is in many parts already super great!

from enrichr_issues.

Hi,

the odds ratio is computed like so:

int totalBgGenes = 20000; // hardcoded
int gmtListSize = length of gene set from library
int numGenelist = length of gene set from user input
int a = numOverlap;
int b = gmtListSize - numOverlap;
int c = numGenelist - numOverlap;
int d = totalBgGenes - numGenelist - gmtListSize + numOverlap;
double oddsRatio = (1.0 * a * d) / Math.max(1.0 * b * c, 1);			

I hope this helps.

Best,
Alex

from enrichr_issues.

Yes thanks! That clarifies it. Will you update the help text accordingly? (I would opt for writing minus and plus as words to make it clear - and/or link the function on GitHub?)

from enrichr_issues.