[BioC] averaging replicates within arrays

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Wed Nov 9 02:11:31 CET 2005

As Dr. Roger Gray (of Heriot-Watt) is fond of saying 

 "If you put one foot in a bucket of boiling hot water and another foot
in a bucket of ice, then you should be comfortable on average".

But if you still want to do this in R, then tapply() might help.

Regards, Adai

On Tue, 2005-11-08 at 22:49 +0000, alex lam (RI) wrote:
> Dear Colleagues,
> Hi, I am a first year PhD student recently started on a project involving microarray data analysis at the Roslin Institute in Scotland. I have managed to follow the limma  vignette in loading the data and performed the default normalization within arrays. On each array, probes of the same genes have been placed in more than one spot. What I would like is to do is to group spots by gene names in MA$genes and calculate the average logratio as the expression level (better still, ignore the spots with zero weight).
> I guess I can dump the data and process it in perl but would like to know how to do this a bit more elegantly in R. Your help is greatly appreciated.
> Many thanks,
> Alex
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