Entering edit mode
4 months ago
Jakpa ▴ 50
I did Ensembl ID to Gene Symbol annotation using
org.Hs.eg.db with this code:
annotn = mapIds(org.Hs.eg.db, keys = rownames(res), keytype = "ENSEMBL", column = "SYMBOL", multiVals = "first")
res is a geneExpression dataFrame that has more than 50,000
ensembleID. but, after running the annotation, about 45% are NAs. i.e, they were not assigned any gene symbol.
org.Hs.eg.db could not properly do the mapping due to the dataset? or my
syntax is not totally correct?
how do I fix this? are there other options?
I dont want to delete the
Ensembl ID with NAs
Hi! Can you show some IDs (
Not all ensembl IDs have an associated gene name, and there are genes with a single gene name, but multiple gene IDs (the joys of gene identifiers).
If you want to ensure the best chance of mapping your gene IDs to the gene symbols make sure you are using the same ensembl release version the gene expression data was generated from. If there isn't an org database associated with that release you could use
biomaRtto convert the IDs instead.
rpolicastro , Thanks for your response. Initially, i did this using
and i got empty
I tried to solve the problem, but i couldnt .
Please, Can you spot any code error?