Question: MA plot interpretation before and after normalization
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gravatar for Expe
22 months ago by
Expe10
Expe10 wrote:

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.

ADD COMMENTlink modified 22 months ago by YaGalbi1.4k • written 22 months ago by Expe10

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?

ADD REPLYlink modified 22 months ago • written 22 months ago by YaGalbi1.4k

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

ADD REPLYlink written 22 months ago by Expe10
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