[BioC] Boxplots, different results?

[J.delasHeras at ed.ac.uk]

Quoting 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?

further to the above, I notice the number of observations is not 
correct when I do (b):

> bpv<-boxplot(MAw$M[,1],MAw$M[,2],MAw$M[,3],plot=FALSE) # case (a)
> bpf<-boxplot(MAw$M ~ col(MAw$M[,1:3]),plot=FALSE)      # case (b)
> bpf$n
[1] 16218 16218 16218
> bpv$n
[1] 9181 9435 9331

the number of spots on these arrays is 10752. Clearly (a) is wrong...

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
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