This is a test version of Biostars. For the public version, visit https://www.biostars.org.
NAs using org.Hs.eg.db for Ensembl ID to Gene Symbol annotation

Hi Everyone,

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.

is that 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 theEnsembl ID with NAs

regards,

rnaseq annotation expression gene r
• 2,278 views • link
updated by rpolicastro rpolicastro • written by Jakpa • Jakpa

Hi! Can you show some IDs (rownames(res))?

• 0 views • link
written by iraun iraun

iraun ,

'ENSG00000288663''ENSG00000288667''ENSG00000288669''ENSG00000288670''ENSG00000288674''ENSG00000288675'

• 0 views • link
written by Jakpa • Jakpa

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 biomaRt to convert the IDs instead.

• 0 views • link
written by rpolicastro rpolicastro

rpolicastro , Thanks for your response. Initially, i did this using biomart

ensid_symbol<-function(ids){
  mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
  genes <- getBM(filters= "ensembl_gene_id", 
                 attributes= c("ensembl_gene_id","hgnc_symbol"),
                 values=ids, mart= mart)
  return(genes)
    }

df <- ensid_symbol(row.names(res_output))

result_df <- as.data.frame(res_output)                 
result_df$ensembl_gene_id <- row.names(result_df)
result_df <- merge(df,result_df, by = "ensembl_gene_id")
resOrdered<-result_df[with(result_df, order(abs(log2FoldChange), padj, decreasing = TRUE)), ]

and i got empty observations with only column names

I tried to solve the problem, but i couldnt .

Please, Can you spot any code error?

• 0 views • link
updated by rpolicastro rpolicastro • written by Jakpa • Jakpa

0 answers

No answers yet.

Log in to answer this question.

More posts like this