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

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.

edger go entrezid
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updated by i.sudbery i.sudbery • written by sarahawan92 • sarahawan92

2 answers

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.

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written by Gordon Smyth Gordon Smyth

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?

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written by sarahawan92 • sarahawan92

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.

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written by i.sudbery i.sudbery

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?

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written by sangi • sangi

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.

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written by i.sudbery i.sudbery

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