I recently started using GOSEQ for the analysis of RNA-Seq results from DESeq2. I have around 37K total genes with ~3K differentialy expressed. I am using mm9 with ensGene ids to run goseq command. It works fine, however gives me a warning :
For 16675 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier.
I would like to know whether excluding these genes has any effect on testing? And whether I should use the use_genes_without_cat=TRUE option to avoid this..
my R version is : 3.1.3 (2015-03-09), and GOSEQ verison is: goseq_1.16.2