What is P-value?
The p-value represents the probability that the correlation measure occurs at random. Therefore, the lower the p-value of G, the more likely this G was not generated at random. This value is calculated using a random permutation of the law matrix (cells are mixed at random) from which the correlation metric is generated. Ten thousand of these random generations are calculated. The proportion of the randomly generated metric that is the same as or higher than the actual metric is the p-value.
The P-value is obtained from moderated t-statistic and after FDR adjustment which is Benjamini and Hochberg’s method to control the false discovery rate. If you select all the genes with p-value less than a given value, say 0.05, as differntially expresed, then the expected proportion of false discovery in the selected group should be less than that value, in this case less than 5%. Among the three statistics, moderated-t, associated p-value and B-statistic, we usually base our gene select on p-value. The p-value will represent an area under a probability curve which is less than or greater than a significance level. The significance level is defined by the user and is normally 0.05 or less and and any P-values below that mark are considered “significant”. P-values do not simple provide you with a “Yes” or “No” answer, they provide a sense of the strength based on the evidence. The lower the p-value, the stronger the evidence.
