[BioC] Correlation analysis of replicates

[K Tre]

Hi Mark,

Thanks for suggesting gene selector package, it might work. I am still
wondering whether it's possible to upload just 2 Affymetrix chips in
R/AffylmGUI and get a correlation coefficient rather than using Excel
or something else. Does anybody know?

Thanks,
Kai

On Thu, Nov 5, 2009 at 7:23 PM, Mark Cowley <m.cowley0 at gmail.com> wrote:
>
> Hi Kai,
> i'm not sure about your first question, but...
> re the correlation coefficient, take a look at the GeneSelector package. In their original paper, they called  the correlation an OrderScore if I recall correctly.
> cheers,
> Mark
> -----------------------------------------------------
> Mark Cowley, PhD
>
> Peter Wills Bioinformatics Centre
> Garvan Institute of Medical Research, Sydney, Australia
> -----------------------------------------------------
>
> On 06/11/2009, at 5:37 AM, K Tre wrote:
>
>> Hi,
>>
>> We are trying to compare affymetrix genelists generated a while back
>> using MAS 5.0 to the new genelists generated using RMA analysis.
>> Previously, we used to perform a comparison expression analysis of the
>> replicates first (3 replicates for each condition) in order to determine the
>> false positive rate. Is there a way to do something similar in RMA just for
>> comparative purposes?
>> Also, is it possible to compare only 2 chips at a time and generate a
>> correlation coefficient? I checked the posting guide but couldn't find a
>> previous email that would answer this question.
>>
>> Any help or pointing where to look is much appreciated,
>> Thanks,
>> Kai
>>
>>        [[alternative HTML version deleted]]
>>
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>