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I have 3224 Ensembl id's as rownames in a dataframe "G". To convert Ensembl ids into Genesymbols I used biomart like following.

library('biomaRt')
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
genes <- rownames(G)
G <-G[,-6]
G_list <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"),values=genes,mart= mart)

Now in G_list I can see only 3200 ensembl ids showing Genesymbols / No Gene_symbols. Why the other 24 ensembl ids are not seen in G_list? If there are no gene_symbol for those 24 ensembl ids it should atleast show "-"

Examples of problematic IDs are: ENSG00000257061, ENSG00000255778, ENSG00000267268. These are not at all shown in G_list (biomaRt). So, I gave them in biodbnet, which seems to handle them.

what is the problem here?

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2 Answers 2

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It looks like you were using an old annotation. The problematic IDs you posted existed in the GRCh37 annotations, but don't in the most recent GRCh38 annotation. For that reason they were excluded. The IDs that have - as symbols don't have associated symbols, but are present in the database.

To use an archived version in biomart:

mart = useDataset("hsapiens_gene_ensembl", useEnsembl(biomart="ensembl", version=84))

That's an example for release 84.

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    $\begingroup$ biomaRt will return NA for genes that are in the database, but don't have symbols. $\endgroup$
    – Ian Sudbery
    Aug 25, 2017 at 12:11
  • $\begingroup$ @IanSudbery Yeah, I'm assuming that OP replaced NA with - at some point. $\endgroup$
    – Devon Ryan
    Aug 25, 2017 at 12:13
  • $\begingroup$ As you said, I thought the same that the problematic ID's are existed in GRCh37. And tried with that too. And among 3224, I found only 3089 in the results. $\endgroup$
    – stack_learner
    Aug 25, 2017 at 12:15
  • $\begingroup$ Those IDs existed in the GRCh38 release 78 annotation (just checked a local GTF), so perhaps they're still GRCh38, but just an older release of it. $\endgroup$
    – Devon Ryan
    Aug 25, 2017 at 12:19
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    $\begingroup$ Just by-the-by, I'm going to guess that any ID that has been retired is unlikely to map to a HGNC symbol. $\endgroup$
    – Ian Sudbery
    Aug 25, 2017 at 13:07
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I used gProfileR where there are no problematic IDs with that. It converted ENSEMBL IDs to Gene_symbols and made my work easier with GO analysis too. There is an R package and also API.

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