How to explain the MA plot for differential expression analysis in RNA-seq data?


Hello guys, I am totally new for RNA-seq data analysis. Here is my dataset background. It has a five controls and five diseased samples. I am wondering is the MA plot good or are there mistakes and how do I interpret this graph. Can anyone guide me on this. Thanks a lot in advance!
enter image description here





Is your plot an MA plot though? The X axis should be log2 as well, yours seems linear. Apply the log2 to make your plot show the data as proper MA plots should.

The normal expectation is that at low A the M is more variable, since the errors are fixed when the values are small the errors are a higher percentage of the signal. This the expectation is that as you go to the right the plot tightens.

Here is an example (from the SeqMonk docs)

enter image description here

"an underlying assumption is that most of the genes would not see any change in their expression; therefore, the majority of the points on the y-axis (M) would be located at 0, since log(1) is 0"

An MA plot with a high number of data points falling above the one threshold on the y-axis would indicate a more significant number of genes being upregulated, while more below −1 would indicate high levels of downregulation in genes. Commonly, MA plots with have a fairly even dispersion relative to the y-axis, which tightens with an increase along the x-axis

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