> Date: Wed, 19 Nov 2008 12:23:36 +0000
> From: Steve Taylor <stephen.taylor@imm.ox.ac.uk>
> Subject: [BioC] Can't load annotations with lumi
> To: Bioconductor <bioconductor@stat.math.ethz.ch>
> Message-ID: <49240548.6070608@imm.ox.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi,
> 
> I am trying to analyse some Illumina data using lumi. I have 
> installed 'lumiHumanAll.db' but when I try and read in the Illumina 
> file it seems to load all the data except the annotation information...
> 
>  > x.lumi<-lumiR(fileName)
> Warning message:
> In addNuId2lumi(x.lumi, lib = lib) :
>    Please provide the annotation file or lumi annotation library!
> 
> If I include the name of the library...
> 
>  > x.lumi<-lumiR(fileName,lib="lumiHumanAll.db")
> Warning messages:
> 1: In addNuId2lumi(x.lumi, lib = lib) :
>    lumiHumanAll.db does not include nuID conversion information!
> 2: In addNuId2lumi(x.lumi, lib = lib) :
>    Please provide the annotation file or lumi annotation library!
> 
>  >  x.lumi
> Summary of BeadStudio output:
>          Illumina Inc. BeadStudio version 3.3.7
>          Normalization = none
>          Array Content = HumanHT-12_V3_0_R1_11283641_A.bgx.xml
>          Error Model = none
>          DateTime = 18/11/2008 18:43
>          Local Settings = en-GB
> 
> Major Operation History:
>              submitted            finished
> 1 2008-11-19 11:57:45 2008-11-19 11:57:57
> 2 2008-11-19 11:57:57 2008-11-19 11:58:00
>                                              command lumiVersion
> 1           lumiR("Sample_Probe_Profile.txt")       1.6.3
> 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh)       1.6.3
> 
> Object Information:
> LumiBatch (storageMode: lockedEnvironment)
> assayData: 48803 features, 24 samples

> 
> My other question is (other than deleting the columns in the source 
> files) if I QC an array and want to exclude it, how do I do that 
> using the LumiBatch object?
> 
> The data is exported from BeadStudio version 3.3.7.
> 
> Thanks for any help,
> 
> Steve
> ------------------------------------------------------------------
> Medical Sciences Division
> Weatherall Institute of Molecular Medicine/Sir William Dunn School
> Oxford University
> 
> 


Dear Steve,
If what you are trying to accomplish is to get the NuID conversions to 
work properly, here is some sample code that I use that works. If I do 
otherwise, I get the errors you mentioned above. This code requires you to 
download the annotation file from the Illumina website and also to check 
that the column names in the BeadStudio export file are properly 
identified in the "annotationColName" specifier:

input_file = "/path/to/your/BeadStudio/file"
mydata.lumi = lumiR(input_file, inputAnnotation = FALSE)
annotationFile = "../../annotation/HumanRef-8_V3_0_R1_11282963_A.txt"
mydata.lumi = addNuId2lumi(x.lumi = mydata.lumi, annotationFile = 
annotationFile, annotationColName=c(sequence="Probe_Sequence", probe = 
"Probe_Id"))

And for your other question, here is how to delete a sample from a 
LumiBatch object:

Say you want to delete sample "A". First find where this sample is:

which(sampleNames(mydata.lumi) == "A")

Then delete it from the Lumi Object:

mydata_reduced.lumi = mydata.lumi[,-30]

where "30" is replaced by whatever response you get to the 
which(sampleNames) query.

Hope that helps,
Kristen Dang
Postdoctoral Associate
Duke Human Vaccine Institute
www.duke.edu/~kd63
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