Differential expression gene
library(MASS)
library(calibrate)
res = read.csv("gene_exp_diff.csv", header = TRUE, sep = ,)
head(res)
Gene_ID log2FoldChange pvalue
1 1/2-SBSRNA4 -9.90259e-01 0.621233
2 A1BG -6.17003e-01 0.314404
3 A1BG-AS1 -1.28873e-01 0.823970
4 A1CF -1.79769e+308 0.346752
5 A2LD1 -1.24245e-01 0.740039
6 A2M -1.29519e-01 0.798185
with(res, plot(log2FoldChange, -log10(pvalue), pch=20, main = "Differential expression gene\nL265P_S21_L008 vs WT_S22_L008", xlim=c(-4,4)))
with(subset(res, pvalue<0.05), points(log2FoldChange, -log10(pvalue), pch=20, col="red"))
mtext(paste("pval = ", 0.05), side = 4, at = -log10(0.05), cex=0.8, line=0.5, las=1)
abline(h = -log10(0.05), col = "blue", lty = 2)
with(subset(res, pvalue<.05 & abs(log2FoldChange)>1), textxy(log2FoldChange, log10(pvalue), labs=Gene_ID, cex=.8))