Question: z-Score vs fold enrichment
gravatar for jenny_keh
4.8 years ago by
United Kingdom
jenny_keh0 wrote:

Hi everyone,

I have performed a GO analysis of microarray data using both GO-Elite and David. I did it in both because some of the genes that are included in DAVID analysis do not appear in GO-Elite. And here comes the confusion! DAVID scores the results based on fold enrichment and GO-Elite based on z-score. What is the difference between these 2 if any?


Thank you in advance!



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ADD COMMENTlink modified 4.8 years ago by mark.ziemann1.2k • written 4.8 years ago by jenny_keh0
gravatar for mark.ziemann
4.8 years ago by
mark.ziemann1.2k wrote:

Hi Jenny. I share your frustration. Keep in mind that some of these databases are more current than other and they will have a different set of array probes and gene ontologies to test against.

With David, you submit a list of genes and the algo looks for enrichments in the ontologies that can be tested with Fisher exact or hypergeometric test. GO-elite is a bit more sophisticated and in addition to Fisher test performs permutations to see how often these enrichments are observed by chance. I would suggest that Go-Elite is a better approach, but I would also suggest to compare it with GSEA (preranked) as the "real" enrichments will be consistent for both methods. 

For fun, try submitting a set of random genes to David a few times and get a feel for false positives.

ADD COMMENTlink written 4.8 years ago by mark.ziemann1.2k
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