Post by DAVID user on Jul 21, 2020 14:35:03 GMT -5
Good afternoon DAVID team,
I have been trying to run my list of diff. expressed genes this afternoon, and I am getting stuck. Some of my genes IDs are listed below. I tried Functional Annotation -> Copy and paste my list (~13,000 up and down genes) -> Gene list. The problem is that none of the gene identifiers that I tried seem to recognize my list (isn't that just the gene symbol?). Anyway, when I tried to convert the list to the standard identifier, it gets stuck in 30% and never finishes. I was able to convert and run a smaller list (<3000 genes), but not my complete list. Even if I split between up and down regulated genes, I have more than 3000 in each list, and it doesn't finish. Is the size of my lists the problem? Any suggestions on how should I run this data? And, what type of identifier should I select to skip the conversion step and run the analysis directly?
Post by DAVID user on Jul 21, 2020 14:35:21 GMT -5
Due to the computational requirements for most tools in DAVID, we do limit lists to 3000 genes which typically meets the needs of most differentially expressed gene lists. There should be a warning that pops up informing users of this and we apologize if it did not.
We also limit the upload of gene symbols to 3000 as well given their ambiguous nature, leading to one symbol mapping to multiple species. You can imagine how quickly a list of thousands of symbols can grow over thousands of species.