[BioC] Analysing multiple-platform gene expression data

[Marc Carlson]

Hi Gabriel,

I would urge caution.  Because even though "on paper" the different
platforms might claim to be using many of the same probe sets, it is
possible to actually measure differences that seem to be caused by
nothing other than the fact that a given probeset was measured on one
chip type vs another. 


  Marc


On 01/26/2011 01:25 AM, gabriel teku wrote:
> Hi Jordi,
> When I said multiple Affy platforms I meant different Affy chips, e.g.
> hgu133a, hgu133plus2.
> Is it OK and possible to remove probes not present in both platforms?
> What are the bilogical/statistical implications of doing this.
>
> Thanks in advance
>
> On Mon, Jan 17, 2011 at 2:45 PM, Jordi Altirriba <altirriba at hotmail.com>wrote:
>
>   
>> Dear Gabriel,
>> We would need more information. What do you mean by different types of
>> Affymetrix platforms? Platforms situated in different places, different
>> machines, different Affymetix chips, etc, etc.
>> Regards,
>>
>> Jordi Altirriba
>>
>>
>> Message: 3
>> Date: Mon, 10 Jan 2011 15:53:43 +0200
>> From: gabriel teku <gabbyteku at gmail.com>
>> To: bioconductor at r-project.org
>> Subject: [BioC] Analysing multiple-platform gene expression data
>> Message-ID:
>> <AANLkTinzi+n2A=D4Nj_H3c4d4P7ruW3HF2BnKsB=vJO_ at mail.gmail.com>
>> Content-Type: text/plain
>>
>> HI All,
>> I'm trying to analyse microarray experiment data in which two types of
>> Affymetrix platforms were used. However, I don't know how to handle these.
>> I'll be great if I could get a heads up right from the beginning in terms
>> of
>> statistics, etc.
>>
>> Thanx
>> Gabriel
>>
>> [[alternative HTML version deleted]]
>>     
> 	[[alternative HTML version deleted]]
>
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