[BioC] Lumi Error

[Pan Du]

Hi John,

What's your sessionInfo()? The latest release version should be 1.8.2. If it
is not, please update it. Tell me more details if there is any further
problem. 


Pan



On 11/5/08 6:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Date: Tue, 4 Nov 2008 14:45:06 +0100
> From: "John Lande" <john.lande77 at gmail.com>
> Subject: Re: [BioC] Lumi Error
> To: bioconductor at stat.math.ethz.ch
> Message-ID:
> <c2ebc3880811040545x2ade67beoecf6b6b36367b6f2 at mail.gmail.com>
> Content-Type: text/plain
> 
> On Tue, Nov 4, 2008 at 12:04 PM, John Lande <john.lande77 at gmail.com> wrote:
> 
>> dear all,
>> 
>> I am using lumi to normalize raw Illumina Data, but when I run the script,
>> I retrive this error. can you help me?
>> 
>> library(lumi)
>> 
>> r=lumiR("gene_expression.txt")
>> 
>> b=lumiB(r, method="bgAdjust")
>> 
>> Perform bgAdjust background correction ...
>> There is no control probe information in the LumiBatch object!
>> No background adjustment will be performed.
>> 
>> thank you
>> 
> 
> maybe it is just a problem of annotation, thereby I added the library
> annotation when I import data:
> 
>> r=lumiR("Breast_86.txt", lib = "lumiHumanIDMapping.db")
> Annotation columns are not available in the data.
> Perform Quality Control assessment of the LumiBatch object ...
> Error in names(mapping.new) <- inputID.bak :
>   'names' attribute [24354] must be the same length as the vector [24350]
> 
> but again another error...
> 
> [[alternative HTML version deleted]]
> 
> 
> 
> ------------------------------
> 
> Message: 13
> Date: Tue, 4 Nov 2008 08:54:54 -0500
> From: "Sean Davis" <sdavis2 at mail.nih.gov>
> Subject: Re: [BioC] Lumi Error
> To: "John Lande" <john.lande77 at gmail.com>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID:
> <264855a00811040554n7c45c42fva93e627b8e8fe586 at mail.gmail.com>
> Content-Type: text/plain
> 
> On Tue, Nov 4, 2008 at 8:45 AM, John Lande <john.lande77 at gmail.com> wrote:
> 
>> On Tue, Nov 4, 2008 at 12:04 PM, John Lande <john.lande77 at gmail.com>
>> wrote:
>> 
>>> dear all,
>>> 
>>> I am using lumi to normalize raw Illumina Data, but when I run the
>> script,
>>> I retrive this error. can you help me?
>>> 
>>> library(lumi)
>>> 
>>> r=lumiR("gene_expression.txt")
>>> 
>>> b=lumiB(r, method="bgAdjust")
>>> 
>>> Perform bgAdjust background correction ...
>>> There is no control probe information in the LumiBatch object!
>>> No background adjustment will be performed.
>>> 
>>> thank you
>>> 
>> 
>> maybe it is just a problem of annotation, thereby I added the library
>> annotation when I import data:
>> 
> 
> No.  It is that you did not include control probe information in the
> exported data from beadstudio, so lumi has no idea what the background is.
> 
> 
>> 
>>> r=lumiR("Breast_86.txt", lib = "lumiHumanIDMapping.db")
>> Annotation columns are not available in the data.
>> Perform Quality Control assessment of the LumiBatch object ...
>> Error in names(mapping.new) <- inputID.bak :
>>  'names' attribute [24354] must be the same length as the vector [24350]
>> 
>> but again another error...
>> 
> 
> You'll need to determine the annotation package that goes with your chip.
> For illumina, there are a number of choices, so you'll have to choose the
> right one based on the chip and the ID that you want to map.  The
> lumiHumanIDMapping.db package simply maps between different human chips and
> does not provide annotation.  What you have tried here cannot work.
> 
> Sean
> 
> [[alternative HTML version deleted]]
> 
>