[BioC] Manufacturer ids in lumiHumanV1

[Sean Davis]

Benjamin Otto wrote:
> Dear bioconductors,
>
> I just installed the lumiHumanV1 package via the biocLite() procedure
> yesterday. The identifiers of the single probes look very strange to me.
> Beside that they don't appear  in the annotation file provided by Illumina
> the name composition itself made me, let me say somehow suspicious! Here
> comes a quick extract. Did someone observe that before?
>
>   
>> xx <- as.list(lumiHumanV1ACCNUM)
>> xx[1:5]
>>     
> $x00WAIBIVaMvS3EVQ0
> [1] NA
>
> $`9iFKOnl5SKK4SnkAS8`
> [1] "NM_032360"
>
> $Ke_INOf6KSdNz6Qeek
> [1] "NM_030945"
>
> $rKBxx.U0SoWkRRVxac
> [1] "NM_025258"
>
> $ilenrd0XnE.4v_3Zec
> [1] NA
>
>   
>> sessionInfo()
>>     
> R version 2.5.0 (2007-04-23) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets" 
> [7] "methods"   "base"     
>
> other attached packages:
> lumiHumanV1        lumi    annotate        mgcv        affy      affyio 
>     "1.2.0"     "1.2.0"    "1.14.1"    "1.3-23"    "1.14.0"     "1.4.0" 
>     Biobase 
>    "1.14.0" 
>   

These IDs are nuIDs.  They are used by the lumi package and are a 
base-64 encoded version of the actual sequence of the probe.  You may 
find that the "illumina...." data packages, rather than the "lumi...." 
data packages have the standard keys.  However, if you are using the 
lumi package for dealing with Illumina data, the "lumi...." data 
packages will work just fine.  Perhaps Pan Du or Simon Lin will fill in 
some more details about why they use nuID.

Sean