Yes, the data is loaded by getControlData, but when I run lumiB I get the
following message:

>addControlData2lumi(controls.matrix,x.lumi)
>lumiB(x.lumi,method='bgAdjust')

"Perform bgAdjust background correction ...
There is no control probe information in the LumiBatch object!
 No background adjustment will be performed."
Thanks
Mali


On Tue, Mar 8, 2011 at 6:06 PM, Pan Du <du4pan1@gmail.com> wrote:

> Hi Mali
>
> The "illuminaControls.txt" file you sent me can be loaded by
> getControlData function without any problem. The message: "Annotation
> columns are not available in the data"  is the print out message by lumiR
> function (called by getControlData function). It's not a warning message,
> just providing some feedback information to the users.
>
> Pan
>
>
> 2011/3/8 mali salmon <shalmom1@gmail.com>
>
> Thanks Pan for your reply.
>> I thought the step for background correction is optional because Lumi
>> assumes the data is already background corrected (according to the user
>> guide). I didn't realize that background correction for illumina data is not
>> a very good idea, thanks for clarifying this.
>> I compared the file I have (attached) with the sample control file in
>> Lumi, and they seem to have the same format.
>> Mali
>>
>>
>>
>> On Tue, Mar 8, 2011 at 5:15 PM, Pan Du <du4pan1@gmail.com> wrote:
>>
>>> Hi Mali
>>>
>>> First of all, the message you showed is not error. It is just a warning
>>> message. There are several background correction methods to select, and the
>>> step of background correction itself is optional.  The VST transformation
>>> can handle the data without background correction. The main affect of
>>> without background correction for Illumina data is that the fold-change
>>> estimation for low expression probes tends to be lower. But actually that is
>>> not bad at all because those low expression and high fold-change probes
>>> usually is more likely to be false positive. This is my personal opinion for
>>> your reference.
>>>
>>> As for the warning message, I guess the format of your data might be
>>> different from the required one. If you would like to, you can send me the
>>> control data file. I will have a brief check for you.
>>>
>>> Hope this is helpful to you,
>>>
>>>
>>> Pan
>>>
>>>
>>>
>>> Date: Tue, 8 Mar 2011 09:30:10 +0200
>>> From: mali salmon <shalmom1@gmail.com>
>>> To: bioconductor@r-project.org
>>> Subject: Re: [BioC] Lumi problem
>>> > Hi All
>>> > I am analysing illumina array data using "Lumi", and I found a problem
>>> with
>>> > adding control data to Lumi.
>>> > I have tried:
>>> >
>>> > >addControlData2lumi("illuminaControls.txt",x.lumi)
>>> > and got the following message:
>>> > "Annotation columns are not available in the data".
>>> >
>>> > Then I tried to create the LumiBatch by specifing the mouse annotation
>>> > library
>>> > >x.lumi<-lumiR("illuminaAll.txt",lib="lumiMouseAll.db")
>>> > >addControlData2lumi("illuminaControls.txt",x.lumi)
>>> >
>>> > but it didn't help, when I try to do background correction, I still get
>>> the
>>> > error:
>>> > "There is no control probe information in the LumiBatch object!
>>> >  No background adjustment will be performed."
>>> >
>>> > Any ideas?
>>> > Thanks
>>> > Mali
>>> >
>>>
>>
>>
>>
>> --
>> Mali Salmon-Divon PhD
>> EMBL European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Cambridge CB10 1SD
>> tel +44 (0)1223 494444
>> fax +44 (0)1223 494468
>>
>
>


-- 
Mali Salmon-Divon PhD
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
tel +44 (0)1223 494444
fax +44 (0)1223 494468

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