How to annoate the probe id to genes in Affymetrix Human Gene 2.0 ST Array [transcript (gene) version ?

How to annoate the probe id to genes the following array

GPL16686    [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]

my data looks like:

            GSM1507802  GSM1507803  GSM1507804
16650001    2.82            2.77            2.50
16650003    3.25            3.71            3.02
16650005    4.72            3.77            2.75
16650007    4.03            4.90            4.36
16650009    1.55            1.86            1.57

I used biomart for annotation. But it's not getting annoated.

mart = useMart("ENSEMBL_MART_ENSEMBL")
mart = useDataset("hsapiens_gene_ensembl", mart)
annotLookup = getBM(mart = mart,
                     attributes = c("affy_hugene_2_0_st_v1",
                                  "ensembl_gene_id",
                                  "gene_biotype",
                                  "external_gene_name"),
                     filter = "affy_hugene_2_0_st_v1",
                     values = rownames(counts)[1:10], uniqueRows=TRUE)

How can Iget these probe ids get annotated?

biomart geo microarray annotation

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updated 2.0 years ago by ultraanfibio •

• written 2.0 years ago by DareDevil

1 answer

You can try with hugene20sttranscriptcluster.db and AnnotationDbi packages

# annotation of transcript clusters (there are often several probes per gene)
anno_eset <- AnnotationDbi::select(hugene20sttranscriptcluster.db,
                                       keys = (featureNames(eset_filtered)),
                                       columns = c("SYMBOL", "GENENAME"),
                                       keytype = "PROBEID")

### remove multi-mapping probes
anno_grouped <- group_by(anno_eset, PROBEID)
anno_summarized <- summarize(anno_grouped, no_of_matches = n_distinct(SYMBOL))
repeated_probes  <- filter(anno_summarized, no_of_matches > 1)
ids_to_exlude <- (featureNames(eset_filtered) %in% repeated_probes$PROBEID)
eset_final <- subset(eset_filtered, !ids_to_exlude)

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written 2.0 years ago by ultraanfibio •