Question: plotMA in deseq2
gravatar for gv
27 days ago by
United States
gv40 wrote:


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))  


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?




ADD COMMENTlink modified 27 days ago by Michael Love20k • written 27 days ago by gv40
gravatar for Michael Love
27 days ago by
Michael Love20k
United States
Michael Love20k wrote:

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

For default values check the help page

ADD COMMENTlink written 27 days ago by Michael Love20k

Hi Michael

Thanks for the reply. It seems like the default for plotMA is 0.1 from this line

plotMA"(object, alpha = 0.1, main = "", xlab = "mean of normalized counts", ylim, MLE = FALSE, ...)

Also I am trying to play with lfcThreshold parameter of the results function(will ask a separate question on it ). In the output file under log2FoldChange column, if the value is 2, does that mean the gene difference between 2 groups being compared is 4 times? Thanks for all your help.

ADD REPLYlink modified 27 days ago by Michael Love20k • written 27 days ago by gv40

Yes, a log2 fold change of 2 means the expression goes up by 4 fold. We explain how to interpret the results in this section of the workflow (the workflow is like an expanded version of the vignette, going at a slower pace):

ADD REPLYlink written 27 days ago by Michael Love20k
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