[BioC] Boxplots, different results?

[J.delasHeras at ed.ac.uk]

Hi,

I am using limma to analyse my cDNA expression arrays (2 channel).

I am looking at boxplots generated from the M values of my arrays (MA = 
product of 'normalizeWithinArrays', but I am not sure I understand the 
syntax and what the 'boxplot' function is doing.

This is because I get slightly different plots if I try (a) or (b) 
below, which
I thought would be equivalent. Am I missing something?

(a)
boxplot(MA$M[,1],MA$M[,2],MA$M[,3])

(b)
boxplot(MAw$M ~ col(MAw$M[,1:3]))

The differences are noticeable on teh spots outside the "whiskers". The 
main box and whiskers themselves *appear* to be the same. I guess some 
defaults must be different when defining the data as a formula or 
explicitly naming the vectors... but I'm not finding an obvious note as 
to which ones they may be?

thanks for your help,

Jose


-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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