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Question: around 2000 Affy probe set IDs cannot be mapped with Ensembl IDs by BiomaRt
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gravatar for haowang0806
5 months ago by
haowang08060 wrote:

Hi everyone,

I have some hgu133a Affymetrix GeneChip microarray data. I would like to annotate them with Ensembl gene identifiers.

I used biomaRt to annotate. However, the result still has 2239 probe sets cannot be mapped by Ensembl gene ID, such as 200026_at, 203341_at, 203877_at and so on. Does anyone also meet some problems? I will appreciate any help.

Thank you.

My codes are as below:

mart<-useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

hgu133aKeys<-keys(hgu133a.db)

getBM(attribute=c("ensembl_gene_id","affy_hg_u133a")

          filters ="affy_hg_u133a"

          values=hgu133aKeys

          mart=mart)

 

Best,

Hao Wang

 

 

ADD COMMENTlink modified 5 months ago by James W. MacDonald45k • written 5 months ago by haowang08060
2
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald45k wrote:

This has more to do with the mappings that are available from Ensembl for a given Affy array than any Bioconductor package. In other words, biomaRt is just fetching the data from Ensembl's Biomart server, and if a given mapping isn't there, it's because it isn't there rather than a problem with the biomaRt package.

If you use the Bioconductor annotation package, you get slightly better mapping success:

> zz <- mapIds(hgu133a.db, keys(hgu133a.db), "ENSEMBL", "PROBEID")
'select()' returned 1:many mapping between keys and columns
> zz[c("200026_at","203341_at","203877_at")]
        200026_at         203341_at         203877_at
"ENSG00000109475" "ENSG00000115816" "ENSG00000099953"
> sum(is.na(zz))
[1] 1505
> zzz <- mapIds(hgu133a.db, keys(hgu133a.db), "ENTREZID", "PROBEID")
'select()' returned 1:many mapping between keys and columns
> sum(is.na(zzz))
[1] 1165

But do note that there ARE things on any Affy array that won't map to either Ensembl nor Entrez Gene, because they aren't recognized as measuring something that is in either of those data bases.

 

ADD COMMENTlink written 5 months ago by James W. MacDonald45k

Thank you for your answer.

ADD REPLYlink written 5 months ago by haowang08060
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