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DDN271F2: (A) Volcano plot of log2 fold-change versus −log10 FDR-corrected P-value for all probes deemed present in at least four of the eight microarrays analyzed. Green lines denote the selected 2-fold change cutoff, while the red line denotes the 0.05 selected FDR-corrected P-value cutoff.
This is the real A in MA plot. In other words, it is the average of two log-scales values: A = (log2(x) + log2(y))/2 = log2(xy)*1/2. Terminology: baseMean: the mean expression of genes in the two groups. log2FoldChange: the log2 fold changes of group 2 compared to group 1. padj: the adjusted p-value of the used statiscal test. fdr
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The red arrows indicate points-of-interest that display both large magnitude fold-changes (x axis) and high statistical significance (-log10 of p value, y axis). The dashed red line shows where p = 0.05 with points above the line having p < 0.05 and points below the line having p > 0.05.