Hi,

In DESeq2, while making  MAPlot for an object obtained by using results function, is there a way to highlight only those genes, whose log2FC values are >= |1|. For example:

ddsMat <- DESeq(ddsMat)

(res.05_FC0<-results(ddsMat,alpha=0.05,lfcThreshold = 0))  

plotMA(res.05_FC0,main="DESeq2_WTGFP_vs_KOHET",ylim=c(-10,10),alpha=0.05)

Now this will show log2FC values which are like 0.80, 0.75, -0.73 also as red. I want to highlight only those values as red which have log2FC values like 1.3,1.2,-1.34 etc i.e >|1|.

Can I do it in the in built function?

Also the default alpha for plotMA is 0.05??

Am i Correct on this ? log2FC of 1.34 from the above output means there is 2^1.34 difference between the groups?

Thanks

There’s no built in way to do this, but the function is pretty simple. 

For default values check the help page

https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/plotMA