[BioC] problem with lumiRatAll.db
fanx0038 at umn.edu
Wed Jan 20 17:56:25 CET 2010
I installed the latest version BioC (2.5) and lumiRatAll.db (1.8.1). But
I still can't find the annotation for some the probes, such as nuID =
Niuq09_43JW4K1SOe4, as I described in the previous email. Any other
R version 2.10.1 (2009-12-14)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 lumiRatAll.db_1.8.1 org.Rn.eg.db_2.3.5 lumiRatIDMapping_1.4.0
 limma_3.2.1 lumi_1.12.2 MASS_7.3-4
 RSQLite_0.8-1 DBI_0.2-5 preprocessCore_1.8.0
 mgcv_1.6-1 affy_1.24.2 annotate_1.24.1
 AnnotationDbi_1.8.1 Biobase_2.6.1
loaded via a namespace (and not attached):
 affyio_1.14.0 grid_2.10.1 lattice_0.17-26
 nlme_3.1-96 tools_2.10.1 xtable_1.5-6
Thanks a lot,
Gilbert Feng wrote:
> Hi, Flora
> It looks you are using the old version lumiMouseAll.db. Please install the
> latest version BioC (2.5) and lumiMouseAll.db(1.8.1).
> If you have any more question or comment, just let me know.
> Thanks for using lumi and lumi annotation packages!
> On 1/20/10 9:40 AM, "Flora Fan" <fanx0038 at umn.edu> wrote:
>> 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.
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