Specificity of MAplot on DEBrowser

[Scientific Stu]

Hello everyone,
I am a new student on DEBrowser.
I carried out a comparative analysis of the expression of my genes, of RNA-seq, and I wanted to do an analysis by MAplot. However, I don't understand what is the unit used by DEBrowser to draw the A axis?
Does anyone have a solution?

 

Thanks !

[CharonY]

Historically the A was used for average intensity (MA-plot were originally used for microarrays back in the days). As they are also used for sequencing analyses, my assumptions that these are normalized read counts of sorts (unit free probably). But my suggestion is to track down the paper where the tool is being described.

[Scientific Stu]

Thank you for your reply.
I've read all of the documentation and it doesn't seem like the axis calculation is specified.

I also think the axis depends on the number of average normalized reads, but I would have liked to know if the axis was displayed in log2/10/x(Mean reads normalized).

 

Thanks.

[CharonY]

Isn't it just a visualization tool and isn't the DE calculations done by Limma and other tools? I would assume that the plot would then be based on whatever those are spitting out, unless you can set how you want to transform the data. But that should be in the original paper.