[BioC] ttest or fold change

[Nitin Jain]

You may try LPE (under developmental packages on Bioconductor),
which is suited for significance analysis for low number of replicates.

Regards,
-Nitin

>
> Hi,
>
> My own calculations have also shown a lack of sensitivity of both
> t-testing and other approaches when we have few replicates.  You
> might be interested in a mixture approach that seems promising.
> See http://www.stat.wisc.edu/~newton/papers/abstracts/tr1074a.html
> for code and a paper.
>
> Michael Newton
>
> p.s. That site contains a major revision of the report I released
>   last January, with code etc recently updated; aiming for
>   Bioconductor soon!
>
>
> On Sat, 13 Dec 2003, Jason Hipp wrote:
>
> > I am comparinga relatively homogeneous cell culture to another that has been treated, and am using RMA.
> >
> > I only have 3 replicates of each.  Would you recommend a 2 tailed equal variance t test?
> > I also thought I read that with such few replicates, a fold change would be better than a t test?
> > If I get a t test of .0001, and a fold change of 1.2, is this a reliable change using RMA?
> >
> > Thanks,
> > Jason
> >
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