[BioC] plotAffyRNAdeg x-axis length of RNA digestion plot

[James W. MacDonald]

Hi Sue,

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

debug(plotAffyRNAdeg)
plotAffyRNAdeg(deg)

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.

Best,

Jim

> 
> Many thanks for your time.
> 
> Sue
> 
> 
> 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()
>>> deg<-AffyRNAdeg(Data[,c(1,2,3,4)])
>>> jpeg(file="RNA_digestion_plot.jpeg")
>>> plotAffyRNAdeg(deg,col=c(1,2,3,4))
>>> labels<-c("E2h rep 1", "E2h rep 2", "E2h rep 3", "E2h rep 4")
>>> legend(5,6,labels,lty=1,col=c(1,2,3,4))
>>> dev.off()
>>>
>>> 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.
>>
>> Best,
>>
>> Jim
>>
>>>
>>>
>>> Thanks
>>>
>>> Sue Jones
>>>
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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


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