vsn2 - update
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear all, thanks to Hans-Ulrich Klein and Tobias Straub for their feedback on the vsn2 function. This was very helpful. I introduced vsn2 for two reasons: 1. clean up of the code, simplification of the user interface and compatibility with the new Expression class, 2. some (as I thought, minor but useful) changes to the numeric optimisation. It seems that in 2. I was overeager in setting the convergence criterion of the likelihood optimiser much tighter than previously in vsn version 1.x. I had found the results better on my test data sets, but it turns out that for certain other datasets (such as those with which Hans-Ulrich and Tobias work), the likelihood landscape has a long, shallow valley (*) and the optimiser runs and runs and runs out into the far end of it, producing extreme parameter estimates that lead to bad behaviour of the transformation for some data points. Hence also the longer running times. The proposed solution is to either - keep using the old vsn() function till the next release OR - upgrade to vsn >= 2.3.5, available here: http://www.bioconductor.org/packages/2.1/bioc/html/vsn.html In this version, the default convergence criteria in vsn2() have been reverted back to how they are in the old vsn() function, and in addition, they can now be set by the user through the argument "optimpar". For the next release, I have a grand plan for a different parameterisation of the model (and the likelihood) that avoids the flat valley problem and that is uniformly easier to numerically optimise :) My apologies to those who have had problems, I hope that overall the package still provides a useful tool - Best wishes Wolfgang (*) PS. This happens when the additive error component is negligible compared to the multiplicate, and hence when the optimal glog-transformation is close to a normal logarithm.
vsn vsn • 618 views
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