[BioC] Boxplots, different results?

ligia at ebi.ac.uk ligia at ebi.ac.uk
Mon Jul 10 18:17:03 CEST 2006

Hi, Jose

I've also noticed this feature some time ago.
It is related with the way they handle missing data.

For example, if you save the output of boxplot in either case, we can see
a = boxplot(MA$M[,1],MA$M[,2],MA$M[,3])
b = boxplot(MAw$M ~ col(MAw$M[,1:3]))

the number of observations is different:


Because option (b) is removing the NA entries that are common to all the
columns in MAw$M, so you'll have less data points in each vector.

However, if you use the command "split" we this will work, giving the same
results as option (a):

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

Best wishes,

> 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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> UK
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