Hi, all

i am very new to bioconductor, now i am analysing data for RNA data based on Illumina TruSeq DNA

Data which i am analysing is GSE36924.

when mapping illumina ID(e.g.ILMN_1651199) to Gene Symbol, many gene symbol resulted in "NA" .

it means i failed to map as below.

ILMN_3311170                 SKCG-1
ILMN_3311175                   <NA>
ILMN_3311180                   <NA>
ILMN_3311185                   <NA>
ILMN_3311190              LINC00173

the script is as below.

library(illuminaHumanv4.db)

genesymbol <-data.frame(Gene=unlist(mget(x = rownames(data),envir = illuminaHumanv4SYMBOL)))

if you know how to match perfectly, would you teach me ?

thanks in advance

I wouldn't use the mget interface, as that is old tech that doesn't necessarily work as you might expect. Instead I would use mapIds.

symbols <- mapIds(illuminaHumanv4.db, rownames(data), "SYMBOL","PROBEID")

which will give you the first instance of any multiple mappings. If you want all the gene symbols you can do

symbold <- mapIds(illuminaHumanv4.db, rownames(data), "SYMBOL","PROBEID", multiVals = "list")

But do note that getting an NA when you use mget can mean one of two things. First, if there are multiple symbols, then mget will return NA, whereas mapIds will not. Second, if the manufacturer doesn't specify a mapping for a given probe to an Entrez Gene ID, then you will get an NA as well. We are just passing on what the manufacturer says, so if they don't map the probe, then we won't either.

symbols <- mapIds(illuminaHumanv4.db, rownames(data), "SYMBOL","PROBEID")

Thank you so much for teaching me a new function of bioconductor.

this code really works well and i can reduce the number of NA for mapping, but still i found approximately 10,000 probe NA among 40,000 probe.

it really means that those illumina ID is not mapped to Gene ?  in this case, i can delete all probe data for NA ?

in such a case, what do you do usually ?

thanks