[BioC] Issues with lumiMouseAll.db vs lumiMouseV1

Cei Abreu-Goodger cei at sanger.ac.uk
Thu May 29 18:39:28 CEST 2008

Hello all,

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:

lumiR("test_sample_gene_profile.txt", lib="lumiMouseAll.db")

Warning messages:
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
(version matched):

lumiR("test_sample_gene_profile.txt", lib="lumiMouseV1")

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:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
[1] lumiMouseV1_1.3.1     lumiMouseAll.db_1.2.0 AnnotationDbi_1.2.0
[4] RSQLite_0.6-8         DBI_0.2-4             lumi_1.6.0
[7] mgcv_1.3-30           affy_1.18.0           preprocessCore_1.2.0
[10] affyio_1.8.0          Biobase_2.0.0

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