[BioC] How to obtain summarized data without normalization

[Rick Frausto]

Hi, 

>From my best understanding, Sean is generally correct...but depending on
your experimental design you may consider using the Ebarrays package, which
would allow you to make some probabilistic statements.

Cheers,
Rick


On 20/12/10 6:25 PM, "Sean Davis" <sdavis2 at mail.nih.gov> wrote:

> On Mon, Dec 13, 2010 at 5:55 PM, Li, Aiguo (NIH/NCI) [E]
> <liai at mail.nih.gov>wrote:
> 
>> Thanks, Jim.
>> 
>> One more question related to p value
>> 
>> I need to generate a fold changes based on only 2 arrays;  I like to get a
>> p values associated with fold changes.  Which package in R allow me to do
>> this?
>> 
>> 
> The best you can do is fold change with only two arrays.  Just rank your
> genes by fold change and talk to the experimentalists about getting some
> replicates.  It isn't really possible or even meaningful to talk about
> p-values with only two arrays.
> 
> Sean
> 
> 
> 
>> Thanks,
>> 
>> AG
>> 
>> 
>> On 12/13/10 1:39 PM, "James W. MacDonald" <jmacdon at med.umich.edu> wrote:
>> 
>> Hi AG,
>> 
>> On 12/10/2010 10:25 AM, Li, Aiguo (NIH/NCI) [E] wrote:
>>> Hi all,
>>> 
>>> I want to get a probeset level data set without mas5 normalization and
>> used the following script.  Could someone tell me this is right or not?
>>> 
>> 
>> Yes.
>> 
>> Best,
>> 
>> Jim
>> 
>> 
>>> affydata<- ReadAffy()
>>> ExprNonorm<-mas5(affydata,normalize=F)
>>> 
>>> Does these script do the background correction? Or only summarize the
>> probeset level data?
>>> 
>>> Thanks,
>>> 
>>> AG
>>> 
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>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
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-- 
Rick Frausto
PhD Candidate
The University of Sydney
School of Molecular Bioscience G08
Camperdown, NSW 2006 AUSTRALIA
ricardo.frausto at sydney.edu.au
Phone: 61 2 9036 5354
Lab of Iain L. Campbell