We have noticed that, in the leaderboard, the value for N never matches the number of modules we have actually submitted. N is always smaller and, so far, it has been off by 17 to 29 modules. We first wondered whether the [3;100] size range might actually be exclusive rather than inclusive, but (i) we do not get any error message, (ii) the difference does not match the number of modules of size 3 or 100 in our submissions. Are any modules discarded during the scoring process?

Created by Dimitri Perrin dperrin
Thanks for the clarification, @daniel.marbach.
Yes this can happen when the Pascal tool does not return a score for a module. The main reason is that not all genes from the networks can be matched to the gene annotation used by Pascal (UCSC protein-coding genes, while the networks come from different sources and used different annotations). We did not remove genes that cannot be matched from the networks, as we wanted to use the original networks for the challenge. Instead, these genes will be removed after loading the gene sets in Pascal, which can result in some modules with 0 genes or just 1 gene that would not be scored. Such modules do not affect the score (they will not be used for multiple testing correction). Best, Daniel
Hi @Sarv, Thanks for your reply. I am in the same situation as @Beethika: I also submit only modules in the specified size range. I have also double-checked after the fact, and there is no module below 3 or above 100 in my submissions. Still, some modules seem to disappear.
Hi, But I have submitted only those modules which are in size range [3,100], still some modules are getting discarded.
Hi, Modules having size out of range [3-100] are discarded during scoring. This is different from the error you might received at the validation. You may get this error only if there is no module in this size range. Sarvenaz
I was also wondering about the same. In my case around 30 of my modules got discarded.

Modules discarded during the scoring process? page is loading…