[BioC] Single slide analysis using Limma

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Fri Dec 30 16:47:27 CET 2005

> 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.

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