[BioC] illumina data

[Mark Dunning]

Hi all,

I would recommend the Probe Profile rather than the Gene Profile. If  
you look at the number of rows in each, you will see that the Gene  
Profile has less rows meaning that it has averaged over the probes  
which map to the same gene. We often see that the probes matching to  
the same gene have inconsistent values so averaging in this way is  
not ideal.

Hope this helps,

Mark

On 8 Aug 2007, at 10:22, Cei Abreu-Goodger wrote:

> I was asking about it in a previous email... Probe Profile data gets
> slightly messed up with the "lumiMouseV1" package, so I would suggest
> sticking to Gene Profile data, for now...
>
> Cei
>
> Yogi Sundaravadanam wrote:
>> Hi all
>>
>>
>>
>> Is it better to use Probe Profile or Gene Profile for illumine  
>> analysis
>> or it doesn’t matter?  I have been using Gene_Profile.csv for  
>> analysis
>> and it seems OK.
>>
>>
>>
>> Any thoughts would be greatly appreicated.
>>
>> Yogi
>>
>>
>>
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>
> -- 
> Cei Abreu-Goodger, PhD
>
> Wellcome Trust Sanger Institute
> Computational and Functional Genomics
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, CB10 1SA, UK
>
>
>
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> The Wellcome Trust Sanger Institute is operated by Genome Research
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