PaGE_5.1 Documentation - the --min_presence command

When a row of data has too many missing values in a condition, you might want to ignore that gene for the comparison involving that condition (such genes introduce greater noise than genes with fewer missing values, and as such cause the algorithm to be more conservative). This parameter tells the algorithm how few non-missing values that must be present in order not to ignore the gene for that comparison.

You can set this value separately for each condition using --min_presence_list.

This command takes one argument of type integer, which must be a positive integer greater than or equal to 2.

Note: If you set this to be higher than actual the number of replicates in some group, the program will complain.

Example:

> perl PaGE_5.1.6.pl --min_presence 4