Hi Longsi,

I guess you ran the code exactly following the vignette. The vignette was
designed for the case of loading pre-saved data, for your case, you read the
data from raw data file, so you should not run the commands:
łload(MyProject.lumi)˛ łdata(MyProject.lumi)˛. I will modify the vignette to
make this clearer.

The commands you need to run are:
> MyFileName <- 'in.txt'
> My.lumi <- lumiR(MyFileName, lib='lumiHumanV1')
> My.lumi  # view the summary of the data
> ## preprocessing and quality control after normalization
> My.lumi.N <- lumiExpresso(My.lumi, QC.evaluation=TRUE)

As for the warning message of duplicated IDs, that is the design problem of
some Illumina chips. Several Illumina probes have different TargetIDs, but
they have exactly the same probe sequence. In this case, we treat them as
the same probe. That is the reason of reporting duplicated IDs.



Pan


       Date: Mon, 07 May 2007 14:27:55 -0400
> From: "Longsi Ran" <longsiran1126@hotmail.com>
> Subject: [BioC] Problem in lumi
> To: bioconductor@stat.math.ethz.ch
> Message-ID: <BAY143-F3079279755A00F55E26C83A6450@phx.gbl>
> Content-Type: text/plain; format=flowed
> 
> Hi,
> 
> When running lumi, I met some problems.  Here is the workflow:
> 
>> >library(lumi)
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> Loading required package: affy
> Loading required package: affyio
> Loading required package: mgcv
> This is mgcv 1.3-23
> Loading required package: annotate
>> >MyFileName <- 'in.txt'
>> >My.lumi <- lumiR(MyFileName, lib='lumiHumanV1')
> Loading required package: lumiHumanV1
> Warning message:
> Duplicated IDs found and were merged! in: addNuId2lumi(x.lumi, lib = lib)
>> >load(MyProject.lumi)
> Error in load(MyProject.lumi) : bad 'file' argument
>> >data(MyProject.lumi)
> Warning message:
> data set 'MyProject.lumi' not found in: data(MyProject.lumi)
> 
> There are 47293 targetIDs with 17 columns in the BeadStudio output text
> file:
> TargetID MIN_Signal-1523532052_A AVG_Signal-1523532052_A
> MAX_Signal-1523532052_A NARRAYS-1523532052_A ARRAY_STDEV-1523532052_A
> BEAD_STDEV-1523532052_A Avg_NBEADS-1523532052_A Detection-1523532052_A
> MIN_Signal-1523532052_C AVG_Signal-1523532052_C MAX_Signal-1523532052_C
> NARRAYS-1523532052_C ARRAY_STDEV-1523532052_C BEAD_STDEV-1523532052_C
> Avg_NBEADS-1523532052_C Detection-1523532052_C
> 
> No Duplicated IDs were found before loading the data.
> 
> Any help will be appreciated.
> 
> Longsi Ran M.D.
> 



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