Dear guys,
May I know if there is some sample code to use to draw the plot like below?
I have DEGs results from limma, does it need to re run use DESeq2 to use plotMA to get this?
Thank you very much!
Dear guys,
May I know if there is some sample code to use to draw the plot like below?
I have DEGs results from limma, does it need to re run use DESeq2 to use plotMA to get this?
Thank you very much!
From you Limma DEG results, you could use glimmaMA
to generate a MA plot as demonstrated in this vignette (https://bioconductor.org/packages/devel/bioc/vignettes/Glimma/inst/doc/limma_edger.html).
Alternatively, given the DEG matrix, you could also useggplot2
with geom_point
to draw the MA plot. Set the aesthetics so that the Y-axis corresponds log2FC and X axis as average log2 expression. Color the points based on if it is upregulated or downregulated (according to your threshold). The code will look something like this:
ggplot(LimmaResult, aes(x=averageExp, y=log2FC)) +
geom_point(aes(color = Significance))
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Thank you very much! This is super helpful! Appreciate!