Post hoc tests for multiple groups

[socanas]

Hi,

I was excited to see that newer versions of methylKit allow more than 2 groups. I currently have 4 groups and have used methylkit to call deferentially methylated regions after tiling. This produced a p and q value for each region.

Is there a post hoc test built in to methylkit to determine which groups are different for a particular region?

Also, is the methylBase object in the order of how the samples were entered from left to right or reordered based on the grouping?

Thanks, Sarah

[alexg9010]

Hi @socanas,

Thanks for using methylKit!

Unfortunately there is no built-in post hoc test functionality, but if you are implementing it for your own purpose we would definitely consider adding it to the package.

The methylBase will be in the same order the samples were given initially, but if you intend to reorder them consider using the reorganize() function.

Best, Alex