I'm still pretty new to R, so your "working's out" are really helpful
for when I have a similar question. I think I've come across other
places that don't make it clear whether PM, MM, or both probe
intensities are being used. Should I report these to the list as and
when I come across them?
Thanks for the help!
Nathan
-----Original Message-----
From: James W. MacDonald [mailto:jmacdon@med.umich.edu]
Sent: Thursday, 26 June 2008 11:51 PM
To: Watson-Haigh, Nathan (LI, Rockhampton)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] AffyBatch boxplot and histograms
Hi Nathan,
Nathan.Watson-Haigh at csiro.au wrote:
> I'm a little confused what values are actually being plotted for
> boxplot() and hist() when an AffyBatch object is passed. Do they
just
> plot the PM probe intensities or the MM probes as well?
>
> Can anyone clarify?
I see why you are confused - the help pages for S4 methods/classes are
IMO not very clear. You can RTFM all you want and still not know what
is
going on, and to a certain extent this is a good example.
So, from ?AffyBatch-class:
boxplot 'signature(x = "AffyBatch")': creates a 'boxplots of log
base 2 intensities. '
hist 'signature(x = "AffyBatch")': creates a plot showing all
the
histograms of the pm,mm or both data. See 'plot.density'
Boxplot remains opaque, whereas hist gives a hint. From ?plot.density:
plot.density package:stats R Documentation
Plot Method for Kernel Density Estimation
Hmm, that's still really opaque, since we have been routed wrong (I
will
fix this man page btw...).
How about ?plotDensity:
Usage:
plotDensity(mat, ylab = "density", xlab="x", type="l", col=1:6,
na.rm = TRUE, ...)
plotDensity.AffyBatch(x, col = 1:6, log = TRUE,
which=c("pm","mm","both"),
ylab = "density",
xlab = NULL, ...)
Aha! So the default is to plot the pm probes, but you can do mm or
both
if you want.
Now for boxplot. How about looking at the method definition directly?
> showMethods(boxplot, class = "AffyBatch", includeDefs = TRUE)
Function: boxplot (package graphics)
x="AffyBatch"
function (x, ...)
{
.local <- function (x, which = "both", range = 0, main, ...)
{
tmp <- description(x)
if (missing(main) && (is(tmp, "MIAME")))
main <- tmp at title
tmp <- unlist(indexProbes(x, which))
tmp <- tmp[seq(1, length(tmp), len = 5000)]
boxplot(data.frame(log2(intensity(x)[tmp, ])), main = main,
range = range, ...)
}
.local(x, ...)
}
So here the default is to plot both pm and mm probes, but you can
choose
pm, mm or both as well.
Best,
Jim
>
> Cheers,
> Nathan
>
> -------------------------------------------------------------
> Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.)
> OCE Post Doctoral Fellow
> CSIRO Livestock Industries
> J M Rendel Laboratory
> Rockhampton
> QLD 4701 Tel: +61 (0)7 4923 8121
> Australia Fax: +61 (0)7 4923 8222
> -------------------------------------------------------------
>
>
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>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
