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jdblischak / singleCellSeq

Batch effects and the effective design of single-cell gene expression studies
http://jdblischak.github.io/singleCellSeq/analysis
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Adding Poisson GLM normalization #4

Closed davidaknowles closed 8 years ago

jdblischak commented 8 years ago

Overall looks good! Please address the few minor changes I noted, and then I'll merge the PR. Please let me know if you have any questions.

jdblischak commented 8 years ago

I merged the PR and made the small edits. It's now live.

https://jdblischak.github.io/singleCellSeq/analysis/poisson-glm-normalization.html

Thanks!

davidaknowles commented 8 years ago

Hi John - thanks for doing this, with traveling and a grant deadline on Friday it was all a bit hectic. Sorry about that, back on solid ground now.

The good news is that the newest CRAN version of rstan (2.9.0) has the variational inference functionality exposed again so it would be easy for you to run the alternative models I coded up. I'll make an .Rmd for that this week.

Happy New Year! Hope all is going well in Chicago and you're not freezing too badly.

On 5 January 2016 at 12:22, John Blischak notifications@github.com wrote:

I merged the PR and made the small edits. It's now live.

https://jdblischak.github.io/singleCellSeq/analysis/poisson-glm-normalization.html

Thanks!

— Reply to this email directly or view it on GitHub https://github.com/jdblischak/singleCellSeq/pull/4#issuecomment-169120997 .

David A. Knowles, Stanford University. E-mail: knowles84@gmail.com Web: http://cs.stanford.edu/~davidknowles/

jdblischak commented 8 years ago

On Mon, Jan 11, 2016 at 12:39 PM, davidaknowles notifications@github.com wrote:

Hi John - thanks for doing this, with traveling and a grant deadline on Friday it was all a bit hectic. Sorry about that, back on solid ground now.

No problem.

The good news is that the newest CRAN version of rstan (2.9.0) has the variational inference functionality exposed again so it would be easy for you to run the alternative models I coded up. I'll make an .Rmd for that this week.

Great!

Happy New Year! Hope all is going well in Chicago and you're not freezing too badly.

Thanks! Happy New Year to you as well. We're surviving the cold for now...