EdgeR for/rev 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 version of the Edge R filter uses the methods described in https://f1000research.com/articles/6-2055/ to set up a version of the EdgeR filter which can be used to detect differences in the ratio of for to rev reads over a probe. It is most commonly used to analyse methlyation data.

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

Unlike the normal EdgeR filter this one does not require that you quantitate your data with raw counts as it will re-do the quantitation internally during the running of the filter.

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
• You can opt to re-sample the raw counts based on the current quantitation. This option allows you to apply post-quantitation correction to your probes and then use the normalised values to re-divide the raw ratio counts so that the statistics use the normalised values.