Question: GOstats gene set size selection
0
gravatar for Assaf Oron
11.4 years ago by
Assaf Oron40
Assaf Oron40 wrote:
Alex hi, I'm not sure whether you can directly prevent the hyperGTest function from testing small gene-sets. It tests all gene-sets as a default. However, you can certainly filter the list of significant gene-sets by set size. The summary() function for the test output has a "categorySize" argument. Suppose the output of your test is called "testresults". Then do: summary(testresults, categorySize=3) to filter out sets of 2 or less genes. My gut feeling is that you won't get significant gene-sets with 2 genes anyway, so to see any appreciable change in your results you'll have to set the threshold higher. The smallest significant set in the vignette example has 7 genes (6 of them marked as significant). Additionally, the summary function itself returns a data frame, one of whose column is "Size", so you can always arrange and filter the gene-set list later as well. Hope this helps, cheers, Assaf
• 310 views
ADD COMMENTlink written 11.4 years ago by Assaf Oron40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 293 users visited in the last hour