

   Dear Georg,

   Please check if your Fold Change values correspond to:

   FC = 2**logRatio (when logRatio >= 0)

   and

   FC = -2**.(-logRatio) (when logRatio < 0)

   logRatio is the difference of means assuming that the means are
log(2) intensities.

   This is the usual way to define fold changes as an intuitive
measure of the level of induction / repression of a gene in a
symmetric scale (with the same absolute values for induced genes and
repressed genes).

   Best,

   Juan Carlos

   Quoting "Hildebrand, Georg" <georg.hildebrand@mpibpc.mpg.de>:

> Hi,
>
> my question is accordin to the library(RankProd) package
> maybe this question is very easy, but i was not able to find an
> satisfying answer.
>
> I created a list of diff. expressed genes with the Rank product
package.
> Everything works well, but in the output of the topgenes() function
i
> do not understand how the fold change is processed.
> Has anyone a hint?
>
> It is not just the difference of the mean like in limma. Even in
the
> papers of breitling there is no good hint.
>
>
> best regards ,
> Georg Hildebrand
> --------------------------------
> Contact/Kontakt:
> --------------------------------
> Abteilung/Dept.:11100ho
> Web: http://circadianrhythms.mpibpc.mpg.de/
> E-mail: georg.hildebrand@mpibpc.mpg.de
>
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