[BioC] Issues with lumiMouseAll.db vs lumiMouseV1
cei at sanger.ac.uk
Thu May 29 18:39:28 CEST 2008
There have been some posts regarding switching to the new
"lumi____All.db" annotation packages. The problem is, if you have
"older" BeadStudio output the probe sequence is not in the files, so the
these packages cannot be initially used:
1: In addNuId2lumi(x.lumi, lib = lib) :
lumiMouseAll.db does not include nuID conversion information!
2: In addNuId2lumi(x.lumi, lib = lib) :
Please provide the annotation file or lumi annotation library!
So, you can either download and specify an Illumina provided csv file
with the probe/target sequence information, or use the older packages
I happen to have many files from this version of BeadStudio, so this
last option seems like a very practical solution to get into the nuID
space... (but you have to install this "old" package)
Any comments or suggestions would be greatly appreciated...
R version 2.7.0 (2008-04-22)
attached base packages:
 stats graphics grDevices datasets tools utils methods
other attached packages:
 lumiMouseV1_1.3.1 lumiMouseAll.db_1.2.0 AnnotationDbi_1.2.0
 RSQLite_0.6-8 DBI_0.2-4 lumi_1.6.0
 mgcv_1.3-30 affy_1.18.0 preprocessCore_1.2.0
 affyio_1.8.0 Biobase_2.0.0
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