On Mon, Dec 13, 2010 at 5:55 PM, Li, Aiguo (NIH/NCI) [E]
<liai@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@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
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