[BioC] Illumina annotation and lumi

Kristen Dang kristen.dang at duke.edu
Thu Oct 16 15:13:04 CEST 2008


Dan Swan <bioinformatics.lists at ...> writes:

> 
> Hi Bioconductors,
> 
> following the lumi vignette I was hoping to analyse some IlluminaHuman
> v3 data, but I'm curious about the resulting annotation - especially
> with regards to the nuIDs.
> 
> briefly:
> 
> > library(lumi)
> > fileName<-'raw_data.txt'
> > x.lumi<-lumiR(fileName, lib='lumiHumanV2')
> > lumi.N.Q <- lumiExpresso(x.lumi)
> 
> If I look at the resulting data:
> 
> iUYoe44olUvV11drzA  7.012843  7.022146  6.981181  7.002568  6.990872  7.009302
> 0006450661          8.052178  8.018692  8.250159  7.993246  7.944218  7.758490
> i4et1wUK5HiCQ0Gra0  7.212793  7.148882  7.113698  7.192300  7.170937  7.034975
> K1gAjeWlSJHV35XDXo  7.012843  7.043321  6.985838  7.084904  7.109322  7.048612
> KXeDlyuUl4jKR6PFEo  7.110156  7.082396  7.129588  7.138857  7.147254  7.109566
> unMWRFJdQ0ZgRIGERU  7.353679  7.364129  7.476052  7.395571  7.355086  7.230908
> QBBnlu7edxepCdCh1c  7.011031  7.009087  6.998372  7.022854  6.983690  7.008475
> 0007510500          7.003781  7.003634  7.070783  6.998263  7.013868  6.958253
> 0004490414          7.034178  6.976611  7.011459  6.961637  7.065312  7.019079
> HkrqGJVElV10AGFF1I  7.204322  7.197918  7.212510  7.023718  7.101016  7.161244
> 0004150270          7.251880  7.256996  7.260095  7.073517  7.111226  7.217829
> KqgniRuCdnr3uYKs9c  7.587018  7.416183  7.402358  7.526966  7.198392  7.245086
> 
> > nuId<-"iUYoe44olUvV11drzA"
> > nuID2targetID(nuId, lib = "lumiHumanV2")
> $iUYoe44olUvV11drzA
> [1] "ILMN_2722"
> 
> but... what are these 000 prefixed numbers?
> 
> > nuId<-"0006370768"
> > nuID2targetID(nuId, lib = "lumiHumanV2")
> $`0006370768`
> character(0)
> 


Dear Dan,
I am guessing that the 000 numbers are probes that exist on the v3 chips but not
the v2 chip. I think you said you are using v3 chips? But your code specifies to
use the v2 library. Thus the v2 library can't assign a nuID? I am not sure...I
have problems getting the nuID conversion to work sometimes. I've found that
doing the following usually works:
1. export file from beadstudio including probeID column (but not target id) and
probe sequence.
2. Download the annotation files from the Illumina website (e.g.
HumanWG-6_V3_0_R1_11282955_A.txt)
3. read in like so:

library(lumi)
input_file = "data.txt";

data.lumiR = lumiR(input_file, inputAnnotation = FALSE)
annotationFile = 'HumanWG-6_V3_0_R1_11282955_A.txt'
data.lumiR = addNuId2lumi(x.lumi = data.lumiR, annotationFile = annotationFile,
annotationColName=c(sequence="Probe_Sequence", probe = "Probe_Id"))

Hope it helps.

Kristen Dang
Postdoctoral Associate
Duke Human Vaccine Institute



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