[BioC] Re-scaling MA plot Y axis in LimmaGUI?

Keith Satterley keith at wehi.edu.au
Wed Nov 30 23:52:27 CET 2005


I'm checking what you say. The resize Window only adjusts the scale of 
the whole plot window, not the scale on either axis.

There isn't a way of adjusting the scales on the axis in limmaGUI, 
though it is being considered as a future modification.

If an M value is not being plotted, try a different background 
correction method. The Subtract method(the default in limmaGUI) may 
produce some negative values, which are hence excluded. Use None 
instead. There will soon be a change to limmaGUI that includes the 
normexp algorithm which is currently available in limma.

Your right about the command line limma program - more features are 
currently available using it. We plan to add more features to the GUI 
programs. Your comments on which ones (other than settable scale 
parameters) are welcome.



J.delasHeras at ed.ac.uk wrote:

>I am using LimmaGUI to analyse my cDNA microarray experiments and 
>produce plots showing particular genes etc. (LimmaGUI 1.3.9 with R 
>Once I make an MA plot, I can easily resize the X axis (A) if I want 
>to,, as the option is given inside the "Resize" menu. But more often I 
>would like to resize the X axis (M). Either to display a number of 
>plots all in the same scale, or because a particular gene of interest 
>is not been shown as it is off scale (in my latest example, the M value 
>for my gene was around 4, but the Y axis was automatically cut at 
>between 2-3, so my gene wasn't shown...).
>Is there a simple way to re-scale the Y axis?
>Yes, it is becoming clear that I should start getting to grips with the 
>command line version of Limma, because of its flexibility... but it 
>will take me a little time and deadlines being what they are... I would 
>really appreciate any help to allow me to sort this from LimmaGUI now.
>Thanks for any help.

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