Handle biological replicates automatically

[roryk]

Hi Yarden,

What about something like this: http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoas/1318514284 for a tack on module at the end to handle biological replicates for calling the event-level differential splicing? I think you might get more uptake of MISO if it handled replicates automatically.

[yarden]

Hi Rory,

Thanks -- yes, definitely, we're working on this actively and plan to add support for biological replicates soon. We're playing with a few principled approaches to pooling and still trying to figure out the best / most general solution.

--Yarden

[roryk]

Sweet, thanks Yarden.

[ramaniak]

Hi Yarden, Just wondering if you have any update on using MISO with biological replicates? I have a set of tumour/normal samples I would like to analyze. Unfortunately, not all of my samples are tumour-normal paired! Any thoughts on how to implement MISO to do a combined analysis of tumour vs normal?

Thanks Arun

[roryk]

Hi Yarden,

@lpantano and I were talking about how to do biological replicates downstream. You're smarter than we are, do you have any suggestions other than the ones we came up with which was a) doing something IDR like or b) checking differences between the distribution of bayes factors in biological replicates for an event? Hope all is going well.