[BioC] using illuminaMousev2BeadID.bd
nac at sanger.ac.uk
Mon Sep 19 13:32:47 CEST 2011
I have installed illuminaMousev2BeadID.bd in order to re annotate my
differentially expressed gene list (annotated with manufacturer
annotation) according to Illumina MouseWGv2 annotation data.
I am rather confused with the procedure as I have never dealt with
annotation packages before.
What I have is a data frame with probeID, IlluminaProbeIds....see
test.txt file) and I want to get rid of all bad data as defined from
Barbosa-Morais et al (2010) .
I guess this annotation package contains only the "good"information and
I would like to use this to clean my txt file and I am not sure where to
Thanks in advance for any pointers/scripts.
R version 2.11.1 (2010-05-31)
 LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
 LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
 LC_MONETARY=C LC_MESSAGES=C
 LC_PAPER=en_GB.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 illuminaMousev2BeadID.db_1.6.1 org.Mm.eg.db_2.4.1
 RSQLite_0.9-1 DBI_0.2-5
 AnnotationDbi_1.10.1 Biobase_2.8.0
loaded via a namespace (and not attached):
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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