# EdgeR Filter

This is an R based filter so will only be available if you have configured R in the SeqMonk preferences and installed the pre-requisite packages

This filter can be used for differential count analysis. It is normally used in RNA-Seq workflows, but can actually be applied to many different experiment types where the underlying data is a set of read counts.

The filter allows you to select two replicate sets with at least two data stores in each and will identify probes whose representation in the two sets differs significantly.

For this filter to run correctly your data must fulfil two criteria

1. Your quantitation must be raw, uncorrected read counts. If you're using the RNA-Seq filter then you must select the "Generate Raw Counts" option. For other probe types you must use the read count quantitation with no normalisation or log transformation applied
2. You must use either all probes, or a representative subset of probes which are not biased by the differences between the two replicate sets your trying to compare

## Options

- You need to two Replicate Sets to compare from the list on the left.
- You need to select a p-value cutoff for the filter
- You can select whether multiple testing correction should be applied to your results. For your p-values to be valid you must leave this box checked