[BioC] limma plots

[Jason Skelton]

Hi

I have a 6 slide experiment

I'd like to be able to plot a MA plot that combines the data from all 
six slides and takes in to consideration duplicates on the slides

I'm currently trying variations of the command
as outlined on page 9 of the Limma users guide
M <- fit$coef
A <- apply(MA$A, 1, mean)
plot(A, M etc......)

However taking into consideration the duplicates.
The lengths differ and the data cannot be plotted (not surprising)

The spacing specified in lm.series & gls.series is 320 for my arrays
so I tried to take this into consideration

A <- apply(MA$A, 1, mean, spacing=320) but of course this doesn't work
although it does seem to except the spacing function as a option ?
the length of A is twice aslong as M
apologies for my limited R knowledge.....

Anyway....
any ideas how I can achieve a merged MA plot from my six slides

basically I'd like to be able to plot this data and identify particular 
spots using identify()

thanks

-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919