In MetaboAnalyst 6.0, Statistical Analysis, One Factor, the Missing Value Estimation step has the following text “Too many missing values will cause difficulties for downstream analysis. There are several different methods for this purpose. The default method replaces all the missing values with a small values (the half of the minimum positive values in the original data) assuming to be the detection limit. Click next if you want to use the default method. The assumption of this approach is that most missing values are caused by low abundance metabolites (i.e. below the detection limit).”
While the menu below that (Step 2) provides options for “Estimate the remaining missing values”, the default is "Replace by LoDs (1/5 of the minimum of the positive value for each variable). " There is no option to use 1/2 of the minimum positive value as the text would suggest
The instruction is mainly an example on a small value as LoD. What used is 1/5 in our current code