change replicate numbers with cummeRbund

Question

[mike]

Hello,

I have seen that while using cummeRbund replicate number starts with zero. I tried changing replicate numbers in read_groups.info (which is generated while running cuffdiff) but gives error while plotting data with cummeRbund. Is there any appropriate way to change replicate numbers?

Please note that I am NOT talking about the labels (-L) in cuffdiff which can be used to specify condition names.

Thanks

[Devon Ryan]

I imagine that you'd need to do that upstream with cuffdiff. Once you're using cummeRbund, all of the statistics and such are already done, so it makes no sense to change group pairings at that point.

[mike]

I don't think that we can change replicate number at cuffdiff stage. Even if its possible, cummeRbund will still assign zero to first replicate.

[Devon Ryan]

You can certainly change your replicate numbers with cuffdiff. You just need to group your samples appropriately when running it. As to how cummeRbund deals with the results, perhaps it has a bug (it wouldn't be the first one).