[BioC] limma plots

Gordon Smyth smyth at wehi.edu.au
Tue Oct 7 19:27:20 MEST 2003

At 06:13 PM 7/10/2003, Jason Skelton wrote:
>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 ?

No it doesn't. When using R, you should always look at the help page for a 
function to see whether it accepts a particular argument. You can't just 
guess. The apply() function is part of R base and doesn't know anything 
about microarrays.

Anyway, you can do what you want using the unwrapdups() function in limma:

A <- rowMeans(unwrapdups(MA$A,ndups=2,spacing=320), na.rm=TRUE)

In the development version of limma, this is done automatically by the 
lmFit() function which stores the average A-values in the fit$Amean component.


>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
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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