[BioC] Single slide analysis using Limma

Naomi Altman naomi at stat.psu.edu
Fri Dec 30 18:13:14 CET 2005

Within slide replication is NOT suitable for statistical testing.  It 
measures only technical variation within the slide, which is usually 
much smaller than any other source of variation.

That is why in limma we use Blocks to handle replicate spots.


At 10:47 AM 12/30/2005, Vincent Carey 525-2265 wrote:

> > A basic principle of statistical analysis of differential expression
> > is to compare differences between conditions to differences among
> > replicates within condition.
> > If you have no replication, you cannot use a statistical method such
> >
> > All you can do is order the differences (M) from largest to smallest,
> > but this does not tell you anything about statistical significance.
>there might be replication of material ON the slide.
>in this case, one should be able to use limma to do the
>within-slide normalization, and then some analysis that
>makes use of the variability among replicate measures
>to obtain something more informative than a raw ranking.
>the original poster will likely have to contact
>a statistician with some R expertise to carry this out.
>but it is a case near the boundary that is worth being
>able to handle.
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

More information about the Bioconductor mailing list