An MA-plot is a plot of log-intensity ratios (M-values) versus log-intensity averages (A-values). See Ritchie et al (2015) for a brief historical review. For two color data objects, a within-array MA-plot is produced with the M and A values computed from the two channels for the specified array. Plot('n', 'o', data=obj) could be plt(x, y) or plt(y, fmt). In such cases, the former interpretation is chosen, but a warning is issued. You may suppress the warning by adding an empty format string plot('n', 'o', ', data=obj). MA plot and Binary logarithm See more » Bioconductor. Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. New!!: MA plot and Bioconductor See more » Bland–Altman plot.
I have a RNA-seq dataset of tumor and control samples. I plotted two MA plots, before and after normalization (plotSmear with Bioconductor). I don't understand how to know it the results are ok just by looking at the shape. My professor explained that if the 'dot cloud' has a trumpet shape, it is good. But then in some exercise examples he shows MA plots with different shapes that are also ok.I would appreciate an explanation for 'dummies' on this as I am a newbie. I forgot to say that I have already read the wikipedia page about MA plots and some articles about RNA-seq with no luck. Thanks in advance.
It would be better to give an image of the plots in question.
Ma Plots Explanation Explained
If you can't provide that then please tell us what are your X and Y axis labels?
Sorry for my late reply. The X label is logCPM and the Y label logFC (tumor-control).