[BioC] using illuminaMousev2BeadID.bd

[Nathalie Conte]

Dear all,
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  
http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html and 
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 
start.
Thanks in advance for any pointers/scripts.
Nathalie

 > sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=C
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] illuminaMousev2BeadID.db_1.6.1 org.Mm.eg.db_2.4.1
[3] RSQLite_0.9-1                  DBI_0.2-5
[5] AnnotationDbi_1.10.1           Biobase_2.8.0

loaded via a namespace (and not attached):
[1] tools_2.11.1







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