I'd like to use CEMiTool for ORA analysis for budding yeast. I downloaded GO gene sets with Enrichment Browser, read it with
read_gmt function and obtained more than 19000 entrez IDs and GO terms. Then, I converted those IDs to gene names and I found many row repeats of gene sets and NAs all over this new GMT file, reaching to around 39,000 rows. I removed those extra rows and ended up with around 3-4 thousand gene sets. But, using
mod_ora on this final GMT file, I get the following error and I don't know why?
No gene set have size > 10 ... --> return NULL... No gene set have size > 10 ... --> return NULL... No gene set have size > 10 ... --> return NULL... Warning messages: 1: In FUN(X[[i]], ...) : Enrichment for module M1 is NULL 2: In FUN(X[[i]], ...) : Enrichment for module M2 is NULL 3: In FUN(X[[i]], ...) : Enrichment for module M3 is NULL 4: In .local(cem, ...) : Enrichment is NULL. Either your gmt file is inadequate or your modules really aren't enriched for any of the pathways in the gmt file.
By the way, initially I couldn't find modules and I changed set_beta to 2 to see if it differs and showed me 3 modules. I don't know what I did was correct and if the current error is related to that or not and how to solve it?
Please help me. Many thanks!