[BioC] problem with lumiRatAll.db
fanx0038 at umn.edu
Wed Jan 20 16:40:20 CET 2010
I am trying to use lumi package to analyze Illumina RatRef-12_V1.
However, about 30% of the probe IDs don't have annotations in
lumiRatAll.db_1.6.1. Is it because the mapping didn't pass the threshold
or am I doing something wrong?
For example, for probe ID ILMN_1355285:
nuID = Niuq09_43JW4K1SOe4
probe seq = GAGGTGGGGTCATTCTTGTGATCTAGCCCGTGAAGGTCCCAGATGCTGTG
manual blast result as well as Illumina annotation file
RatRef-12_V1_0_R3_11222119_A.txt shows that it mapped to A4galt.
But when I do getSYMBOL, no symbol was returned.
> x<- lumiRatAllACCNUM
> mapped_probes <- mappedkeys(x)
> ind<-c(1:16134)[mapped_probes == "Niuq09_43JW4K1SOe4"]
It returned integer(0)
How can I annotate these IDs? Can I keep the original gene symbols that
were generated from GenomeStudio version 1.0.6 as identifiers in lumi
Here is the sessionInfo()
R version 2.9.1 (2009-06-26)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 lumiRatAll.db_1.6.1 lumiRatV1_1.2.0 beadarray_1.12.1
 hwriter_1.1 lumiRatIDMapping_1.2.1 limma_2.18.0
 lumi_1.10.2 RSQLite_0.7-1 DBI_0.2-4
 preprocessCore_1.6.0 mgcv_1.5-5 affy_1.22.0
 annotate_1.22.0 AnnotationDbi_1.6.0 Biobase_2.4.1
loaded via a namespace (and not attached):
 affyio_1.12.0 grid_2.9.1 lattice_0.17-25 nlme_3.1-92
 tools_2.9.1 xtable_1.5-5
Your help will be greatly appreciated.
Biostatistics and Informatics
Masonic Cancer Center, University of Minnesota
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