[BioC] NuIDs not found
ebs15242 at gmail.com
Fri May 4 23:26:51 CEST 2012
I am using minfi to analyze some illumina 450K arrays.
I have a list of differentially methylated positions that
I want to convert to gene names, or something useful.
There's no information on annotation in the minfi
manual, but I can get the sequence from
I found the pdf "Resolve the inconsistency of
Illumina identifiers through nuID", which sounds
like it should help me do what want.
If I understand correctly, all I have to do is convert my
sequence to a nuID, and then conver the nuID to a
refseq or gene symbol or what have you.
I can do the first part easily:
>ProbeInfo <- getProbeInfo(IlluminaHumanMethylation450kmanifest, type ="I")
> head(dmp, n=1)
intercept f pval qval
cg07466271 2.232301 39.90621 1.447446e-09 0.0006144155
> which(ProbeInfo$Name == "cg07466271")
Name AddressA AddressB Color NextBase
293109 cg07466271 49719346 67746443 Red A
293109 TAACCCGAACCCCGCTTCAAATACACAACAAATTCCTTATAAAAACCTCG 2
Great, now I have my nuID. The problem occurs when I try to convert this
into something useful:
> if(require(lumiHumanIDMapping)) nuID2RefSeqID("ZwVAVR9AxEED18wAXQ", lib.mapping='lumiHumanIDMapping')
The provided names of filterTh does not match the field names of
No filtering will be performed.
In getNuIDMappingInfo(nuID, lib.mapping = lib.mapping) :
No matches were found!
I also tried it with 'lumiHumanAll.db', and got the same result:
> getSYMBOL("ZwVAVR9AxEED18wAXQ", 'lumiHumanAll.db')
I get the same thing if I try it with the "IlluminaHumanMethylation450k.db"
> getSYMBOL("ZwVAVR9AxEED18wAXQ", 'IlluminaHumanMethylation450k.db')
What's going on here?
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