User: wwu222

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wwu2220
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Posts by wwu222

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Comment: C: questions regarding design that is similar to "Group-specific condition effects,
... Thank you very much for all your answers, Dr. Love. They are really helpful! ...
written 10 weeks ago by wwu2220
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Comment: C: questions regarding design that is similar to "Group-specific condition effects,
... Thanks, Dr. Love.  I think 3) is pairwise compare the time effect, but what I want is pairwise compare post treatment effect (with / without adjust baseline level).  Sorry, I understand you are very busy and I may be confused at some point. I really appreciate your time and help! "3) Yes, you can ...
written 10 weeks ago by wwu2220
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Comment: C: questions regarding design that is similar to "Group-specific condition effects,
... Thanks, Dr. Love. I may not be clear, I will consult a statistician with alternative statistical approach.  Regarding the "pairwise comparisons with Wald tests " you mentioned earlier,  do I have to perform a separate model or I can extract results using contrast from full model? If latter, can you ...
written 10 weeks ago by wwu2220
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Comment: C: questions regarding design that is similar to "Group-specific condition effects,
... Hi Dr. Love, Thank you very much! I guess LRT couldn't answer my question. Sorry to bother you again. But considering a simpler pre-post treatment design, and I want to implement a ANCOVA model like "post ~ treatment + pre" into DESeq2 work frame, what is the best way to do it ? Because I know DESe ...
written 10 weeks ago by wwu2220
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Comment: C: questions regarding design that is similar to "Group-specific condition effects,
... Dear Dr. Love, Thank you very much for your quick response. Now I know what to do regarding question #1, 3 , 4 with the information and suggestion you provided. For question #2, I have tried the LRT you suggested, my workflow is as below: mm_full = model.matrix(~treatment + treatment:patient.n + ...
written 10 weeks ago by wwu2220
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questions regarding design that is similar to "Group-specific condition effects, individuals nested within groups"
... Dear DESeq2 developer, Thank your very much for this great tool! I have a design that is similar to the one mentioned in deseq2 user guide "Group-specific condition effects, individuals nested within groups" http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#group-spe ...
deseq2 written 10 weeks ago by wwu2220 • updated 10 weeks ago by Michael Love22k

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