Differential analysis & tests / MA plot
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Each point is a gene: the x-axis is mean expression (log scale) and the y-axis the log2 fold change; dashed lines mark ± the |log2FC| threshold.
An MA plot checks whether results depend on expression level: fold changes of low-count genes scatter more (a funnel on the left), and a shift away from 0 among highly expressed genes can point to a normalisation problem.
Red points are up and blue points down (passing both the adjusted-P and fold-change thresholds); grey points are not significant. Keep thresholds identical to those in your methods.
Use log2(x + 1) for DESeq2 baseMean; limma AveExpr and edgeR logCPM are already on a log scale, so choose “none”.
Dudoit et al. (2002) Stat Sin 12:111 (MA plot); Love, Huber & Anders (2014) Genome Biol 15:550 (DESeq2 baseMean). The plot does not recompute differential expression; it shows the values in your table.
Up to 200,000 genes.
Send us your data and research question and you will receive a written plan within 1 working day: analysis steps, parameter rationale, deliverables and timeline. Quoted per project.