[BioC] Analysing multiple-platform gene expression data

[Kauer Max]

Hi,
along the same lines I wondered if one can take the z-scores from the barcode() function in the frma package. From my understanding these scores give a "distance" from the empirically defined value of no expression (separately for hgu133a and hgu133plus2), so in theory these could be comparable between platforms (?)
Does anybody have an opinion on that?

Best,
Max



-----Ursprüngliche Nachricht-----
Von: bioconductor-bounces at r-project.org im Auftrag von Marc Carlson
Gesendet: Mi 26.01.2011 18:45
An: bioconductor at r-project.org
Betreff: Re: [BioC] Analysing multiple-platform gene expression data
 
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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