has part preceded by is about denotes is_specified_input_of is_specified_output_of gene expression scatter plot differential expression analysis data transformation FWER adjusted p-value q-value logarithmic transformation gene list visualization x-axis y-axis volcano plot Orlaith Burke Alejandra Gonzalez-Beltran Philippe Rocca-Serra http://en.wikipedia.org/wiki/Volcano_plot_(statistics) volcano plot is a kind of scatter plot which graphs the negative log of the p-value (significance) on the y-axis versus log2 of fold-change between 2 conditions on the x-axis. It is a popular method for visualizing differential occurence of variables between 2 conditions. volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, ...) http://rss.acs.unt.edu/Rdoc/library/limma/html/volcanoplot.html fold change p-value ready for release