[BioC] plotAffyRNAdeg x-axis length of RNA digestion plot
James W. MacDonald
jmacdon at med.umich.edu
Wed Jun 14 20:09:38 CEST 2006
Please don't respond only to me. I may actually say something brilliant
one day, and would like it saved for posterity on the archives of the
listserv ;-D. Seriously though, you should always keep responses on the
list so people can (possibly) find answers to their questions.
Sue Jones wrote:
> Hi James
> Thanks for replying - if the x-axis is set automatically - how come
> it comes up short in my case? I get the figure I attach ...
Good question. You might try
and step through the function to see what xlim values are being set. I
have never seen a plot like the one you get (and actually don't know of
an Affy chip with 14 probes per probeset), so am not sure why you are
getting these results.
> Also I am slightly concerned that I do not have smoother lines on the
> plot -
> many I have seen in publications are straightish lines - should I just
> be using PM data for this plot?
By default you *are* using PM data.
> But I am right its not the slopes of the lines is the key but the fact that
> the shapes should all be similar across the arrays?
I have never been bothered by the shape of these plots - the only thing
I look for is consistent slopes between the samples. Averaging the PM
probes based on their position in the probeset (across all probesets) is
not biologically sensical, so I don't think the shape of the lines has
any meaning. It's just a way to estimate the degradation of mRNA, and
possibly the quality of the IVT step.
> Many thanks for your time.
> On Wed, 14 Jun 2006, James W. MacDonald wrote:
>> Hi Sue,
>> Sue Jones wrote:
>>> I am using the plotAffyRNAdeg function from affy to create a RNA
>>> digestion plot. I use the following code
>>> Data <- ReadAffy()
>>> labels<-c("E2h rep 1", "E2h rep 2", "E2h rep 3", "E2h rep 4")
>>> The problem I have is that the x-axis is too short (only extends
>>> 0-10) and the lines extend over the end. How do I extend the x-axis
>>> up to 15 as I have 13 probes?
>> The xlim argument is automatically set in the plotAffyRNAdeg()
>> function, so you won't be able to extend it without doing some
>> hacking. You can either copy and paste the function into an editor,
>> change it to your liking and then source() it back in, or if you can
>> install source packages, you can change the source .R file and then
>> re-build the package.
>> Of course this is a bit of work to just make this slight change.
>> You might also want to add width = 700, height = 700 (or something
>> similar) to your call to jpeg(), which will make the resulting plot a
>> reasonable size.
>>> Sue Jones
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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