## PaGE_5.1 Documentation - the `--paired` command

This concept is best illustrated by example. Suppose that two tissue types, type 1 and type 2, are assayed from several different animals. Suppose that a gene is two-fold higher in tissue type 2 than in tissue type 1, but that its intensity level differs greatly from animal to animal. So for example in animal 1 it might be 10 in tissue 1 and 20 in tissue 2, while in animal 2 it is 100 in tissue 1 and 200 in tissue 2. It is a consistently two-fold change in each animal, however this gene might only be found by an approrpriate paired analysis. This is because as unpaired data it has very large variance.

If your data is naturally paired and you suspect an effect of this type, then set this option.

**Note 1**: Both one-channel and two-channel data can be paired. But "paired" makes no sense in the case of a

direct comparison design.

**Note 2**: If using the

`--tstat` option together with the

`--paired` option, the 2-sample

*t*-statistic is replaced by the 1-sample

*t*-statistic. If using the

`--means` option with the

`--paired` option then the ratio of the means is replaced by the geometric mean of the ratios of the paired intensities. See

`--tstat` and

`--means` for more details on the statistics.

**Note 3**: A different permutation scheme is used in the paired case as opposed to the unpaired case. See

`--num_permutations` for more details on the permutation schemes..

This command takes no arguments.

### Example:

> perl PaGE_5.1.6.pl --paired