[BioC] Mouse.lumi problems

[Pan Du]

Hi Anand,

We have updated the Mouse.lumi and Human.lumi packages. The new packages are
named as lumiMouseV1, lumiHumanV1 (for human version 1 chips) and
lumiHumanV2 (for human version 2 chips). An annotation package for the
Illumina Rat chip has also been produced. I will upload them to Bioconductor
in this or next week.
The packages are built using Annbuilder. The mapping between the probe and
RefSeq or Unigene Ids are still based on RefSeq and Unigene annotations
provided by Illumina company. Our future plan is to directly blast against
the latest genome builds and get the mapping between the probes and RefSeq
Ids.

Thanks for reporting the problem.

Pan


On 1/22/07 5:11 PM, "Anand C. Patel" <acpatel at usa.net> wrote:

> Mouse.lumi does not appear to work correctly -- it does not appear to
> have the Mouse.lumiTARGETID2NUID variable in the environment.
> Human.lumi does, Mouse.lumi doesn't.
> 
> Also, for clarification, are either of the new Illumina annotation
> packages new annotations against more recent genome builds, or are
> they just packaging via AnnBuilder (et al) of the Illumina manifest/
> annotation files)?
> 
> Thanks,
> Anand C. Patel, MD
> Washington University School of Medicine
> acpatel at usa.net
> 
> 


---------------------------------------------------
Pan Du, PhD
Research Associate / Senior Bioinformatics Analyst
Robert H. Lurie Comprehensive Cancer Center
Northwestern University
Chicago, IL 60611
Office (312)695-4781
dupan at northwestern.edu