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

The illumHumanv1 and illumMousev1 annotation packages are made using the RefSeq IDs from the Illumina manifest files. Lynn Amon University of Washington Anand C. Patel 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 > >

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