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
