[BioC] Merging bioconductor lumi annotations with lumi output

[Pan Du]

Hi Thomas

You can change the default inputted annotation columns by setting the
"annotationColumn" parameter of lumiR function. These annotation information
will be kept in the "featureData" of ExpressionSet (or LumiBatch) object.

One thing I am not sure is what kind of IDs is used for your GenomeStudio
output data. The Illumina Probe ID, like "ILMNxxx", is recommended. In quite
a few cases, I found people using the Illumina address IDs as the probe ids,
which will cause problems in ID mapping. If you would like to, you can send
top 50 or 100 rows of your data file to me. But I will be out of town for a
conference in the next few days, my reply may delay.

Thanks for reporting the problem.


Pan


On 12/16/10 9:41 AM, "gilbert feng" <g-feng at northwestern.edu> wrote:
> ---------------------------------
> Subject: [BioC]  Merging bioconductor lumi annotations with lumi output
> From:    "Thomas Hampton" <thomas.h.hampton at dartmouth.edu>
> Date:    Thu, December 16, 2010 9:17 am
> To:      bioconductor at r-project.org
> ------------------------------------------------------------------------------
> ------
> 
> Our core has produced raw lumi output for me that includes these
> annotation columns:
> 
> [51] "SEARCH_KEY"                   "UNIGENE_ID"
> [53] "ENTREZ_GENE_ID"               "ACCESSION"
> [55] "SYMBOL"                       "PROBE_ID"
> [57] "DEFINITION"                   "X"
> 
>   lumiR reads the following annotation columns:
> 
> ACCESSION, SYMBOL,
> PROBE START, CHROMOSOME, PROBE CHR ORIENTATION, PROBE COORDINATES,
> DEFINITION.
> 
> Perhaps since these are not there, I get this message:
> 
> Please provide the annotation file or lumi annotation library!
> 
> What is unclear to me, having read the lumi documentation, is whether
> I can
> avoid this message by just adding bioconductor annotations in. I tried
> it like this
> 
>> data <- lumiR("FinalReport.txt", lib.mapping = "lumiHumanIDMapping")
> 
> Warning message:
> In addNuID2lumi(x.lumi, lib.mapping = lib.mapping) :
>    More than 500 identifiers cannot be found in the
> library:lumiHumanIDMapping!
>   The provided library might be wrong or outdated!
> 
> 
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
> [1] lumiHumanIDMapping_1.8.0 RSQLite_0.9-4            DBI_0.2-5
> [4] AnnotationDbi_1.12.0     lumi_2.2.0               Biobase_2.10.0
> 
> loaded via a namespace (and not attached):
>   [1] affy_1.28.0           affyio_1.18.0         annotate_1.28.0
>   [4] grid_2.12.0           hdrcde_2.15           KernSmooth_2.23-4
>   [7] lattice_0.19-13       MASS_7.3-8            Matrix_0.999375-44
> [10] methylumi_1.6.1       mgcv_1.6-2            nlme_3.1-97
> [13] preprocessCore_1.12.0 tcltk_2.12.0          xtable_1.5-6
> 
> 
> 
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> 
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