Good morning to everyone, I'm trying to use the function goana to run a GO enrichment analysis after performing the workflow RnaSeqGeneEdgeRQL. I obtained a list of DE genes with the function glmQLFTest (on the left), and shortly after I decided to use glmTreat as well (on the right), to obtain a more limited dataset. I picked a threshold of logFC > 1.5.
Here is the result
I performed a further GO enrichment analysis on the DE genes.
I used the result of the function glmTreat at first, but what I obtained is an error:
data frame with 0 columns and 0 rows No DE genes
(is the dataset too small to perform a statistically significant GO enrichment analysis?). This just works fine while I try to compare other conditions from which a higher number of genes is obtained.
I also tried to make the function glmTreat work like glmQLFTest, like suggested in the pipeline. I set
tr <- glmTreat(fit, contrast=B.LvsP, lfc=0)
And I obtain the same number of DE genes I did for glmQLFTest. Everything works fine, till I try to use goana again on this specific object, where I obtain a list of GO terms showing p values of 1 in the columns. I guess the test for some reason doesn't work...
How can I solve this problem and perform a GO enrichment analysis? Did I do anything wrong with the two functions? Thanks in advance!