I have 2 questions I hope from your precious time you will try to solve my queries:
1) Firstly my dataset is already processed it is not RAW. So I retrieved boxplot of samples successfully by using R. Then next day I identified DEGs by using LIMMA and GEOquery packages and the adj. P.val was set as < 0.5 (I know mostly people prefer 0.05 value but in my case when I put 0.05 so I don't get any result while when I put <0.5 I get probe ids and all the desired data) After that I identified DEGs. The question is this that do I choose a correct approach can I lead this DEGs towards enrichment analysis and secondly as I choose 0.5 val. for P.adj/fdr how to jusitfy it as I am new to this I try to read so many papers regarding this but still I am not able to justify the scoring criteria of fdr is it acceptable to choose fr/adj.pval<0.5.
2) In my case I got 150 down regulated genes and and 95 up regualted genes so collectively I got 245 DEGs. The question is that should I consider up an down regulated genes separately for enrichment analysis including GO, KEGG and TF analysis or can I collectively calculate Enrichment analysis of all DEGs (it includes up and down regulated genes).
I try to make my questions crystal clear still if there is any mistake so sorry for the inconvenience.
I just want to know in 1st query is my approach is correct and in 2nd query I want to know that what is the correct approach or mostly used approach for enrichment analysis (using DEGs collectively or up and down regulated genes separately) I try to search literature and read many posts on biostar and bioconductor as well but still it is not clear to me.
Thank you in advance.