limma结果按logFC排序是按照logFC的绝对值排序

提取limma差异结果时按照logFC的结果进行排序，即如下代码

DEP = topTable(fit, adjust="BH",n=Inf,sort.by="logFC",coef = "Tumor-Normal")

结果发现跑了两次样品，同一个代码结果的排序不一样，一个是logFC值为正的排序在前，一个是logFC值为负的结果在前，仔细观察后发现，排序还是正负混着来的 image.png

help文档中关于topTable函数中"sort.by"参数的解释是

character string specifying which statistic to rank the genes by. Possible values for topTable are "logFC", "AveExpr", "t", "P", "p", "B" or "none". (Permitted synonyms are "M" for "logFC", "A" or "Amean" for "AveExpr", "T" for "t" and "p" for "P".) Possible values for topTableF are "F" or "none". topTreat accepts the same values as topTable except for "B".

感觉这里面也没太说清楚，这里的rank其实是按logFC绝对值的数值来进行排序的，而不是我们通常理解的先正数值再负数值