MA plot interpretation before and after normalization
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7.0 years ago
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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.

RNA-Seq MA-plot interpretation explanation • 3.7k views
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It would be better to give an image of the plots in question.

If you can't provide that then please tell us what are your X and Y axis labels?

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Sorry for my late reply. The X label is logCPM and the Y label logFC (tumor-control).

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