For Gene ontology analysis in R by using edge R and limma

Question

[sarahawan92]

I am using R studio for the analysis of RNA-seq data related to my research work. I have done my differential analysis and now trying to do GO analysis. Through my reading, I came to understand that is it necessary to link gene symbols to their definite IDS. As "gonna function" is not working .

If it is so then please tell me how I convert my gene list which is (15481) to Enterzids.

Thanks.

Answer 1

[Gordon Smyth]

You can convert gene symbols to Entrez Ids either using the appropriate organism package (e.g., org.Hs.eg.db or org.Mm.eg.db) or by using the limma function alias2SymbolUsingNCBI.

[sarahawan92]

Thank you. Can I use this recommended function after performing "glmFtest" and "glmtreat".If so, can this recommended function help me to perform GO analysis?

[i.sudbery]

Hi @sarahawan92 welcome to the community. When you would like to ask more detail about a posted answer, please use the comment function. This keeps the threads clean and useful for future users.

Answer 2

[sangi]

I used edgeR limma and voom and have a differential expression list but I could use gonna as I didn't find my organism package, apple (Malus domestica). How can I proceed with GO?

[i.sudbery]

Dear sangeetasapkota25 wellcome to the community. This is a seperate question to the one the OP had. Can you please post this as a new question on the forum where you might have a chance that someone who knows the answer will see it.