[BioC] difference between illuminaHumanv1 and lumiHumanV1

[Wolfgang Huber]

Hi Burak

> Is there a difference between illuminaHumanv1 and lumiHumanV1 packages in terms of content?
> Thanks a lot
> -burak

Here is the situation afaiCs for illuminaHumanv2 and lumiHumanV2 packages:

- in lumiHumanV2, annotation environments are indexed by Pan Du's nuID
[1], which correspond 1:1 to reporter sequence IDs, and a translation
table is provided to Illumina *Probe* IDs. AfaIu, the package authors do
their own mapping of reporter sequences to the transcriptome.


- in illuminaHumanv2, annotation environments are indexed by the
Illumina *target* ID, which correspond to the intended (by Illumina)
target gene. See Lynn's message. With the current package version
1.4.0., the function illuminaHumanv2() returns strange "quality control"
results about "Probe number missmatch".

In both cases, I have not found documentation of the quality and
uniqueness of the matches of the reporters to the transcriptome.


[1] Du, P., Kibbe, W.A. and Link, S.M., "nuID: A universal naming
schema of oligonucleotides for Illumina, Affymetrix, and other
microarrays", submitted.


Best wishes
 Wolfgang

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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber