Re-scaling MA plot Y axis in LimmaGUI?
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@jdelasherasedacuk-1189
Last seen 6.2 years ago
United Kingdom
Hi Keith, thanks for your reply. > I'm checking what you say. The resize Window only adjusts the scale of > the whole plot window, not the scale on either axis. The resize menu in the latest limmaGUI (July 2005) gives you two options: "resize window" (whole plot) and also "resize horizontal (A) axis". > There isn't a way of adjusting the scales on the axis in limmaGUI, > though it is being considered as a future modification. That would be a very welcome modification, by me at least! :-) > 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. The values that are not shown are a couple of high values. This is in an experiment with only two slides at present. The combined MA plot omits the spot of a gene I am interested in, and the M values on the Y axis range between roughly -4 to +4. The individual MA plot for each slide does show those spots, and the scales range between about -7 to 4 (my gene shows M about -6 here) , and about -4 to 6 (my gene here shows M about 6). I used between array normalisation (scale). On the exported toptable, the M value is 4.69, which appears to be *just* outside the range plotted by Limma. It's as if the spot were discarded, yet it appears at the top pof my differentially expressed genes (ranked by B statistic), with B=7.55 and P=0.0016 (Holm-adjusted). I am not too worried about the P/B values at present as it's just two slides comparing samples that are in general quite similar, as I add more replicate experiments I am sure the P values will tighten up. But that top gene does appear clearly different, and it's got good spot morphology and intensity etc, everything seems fine (as far as I can tell)... so why is it not plotted? (shrug) > 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. I'm planning to move to limma, but the GUI version is very useful too. Personally I would like to see an option to resize the plots, deciding what range to plot separately for each axis. Also, there's one minor niggle that perhaps it can easily be cured? When I start a new analysis, I enter a particular spot types file. After I see the results, I might want to add further spots, or eliminate others, especially for display purposes on MA plots. I can do that within LimmaGUI, but I wish those changes could be saved. At present it doesn't save them, it sticks to teh original definition for the Spot Types. Having the option to display colour-coded spots on MM plots would also be very useful. More? Okay, one more... ;-) When I use the Image array plot (to display raw intensities, or ratios, or backgrounds, etc), I wish the plot would corresponded to the layout of the slide. It doesn't seem to right now. For instance, I am using arrays with 24 blocks, arranged in 2 metacolumns and 12 metarows. The Image array plot shows all 24 blocks correctly, but arranged in a 4x6 grid. Which is okay to check each block, but slide-wide patterns in background intensities are not as easily seen. I am very satisfied with LimmaGUI as it is and I think you guys have done an excellent job. I hope my suggestions are not taken as "complaints" :-) because they're not! Thanks for all 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 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK
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@jdelasherasedacuk-1189
Last seen 6.2 years ago
United Kingdom
Quoting Keith Satterley <keith at="" wehi.edu.au="">: > 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 I forgot to add to this that this doesn't seem to be the problem. At first I thought of this possibility, as that particular gene shows no signal above background in one channel (it's a gene that is normally silent but I can activate after a treatment)... but even using no background substraction doesn't bring it into view. It surprises me, as it does appear in the toptable, first of the list, in fact, so I guess Limma doesn't just remove it... yours sincerely puzzled, 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 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK
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