[BioC] limma plots

Jason Skelton jps at sanger.ac.uk
Tue Oct 7 10:13:27 MEST 2003


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.....

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()


Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
CB10 1SA

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

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