User: wwu222

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wwu2220
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Posts by wwu222

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to analyze RNAseq data with multiple treatment groups and each subject has p
... Thank you, Dr. Love. You are always so nice! ...
written 8 weeks ago by wwu2220
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Comment: C: How to analyze RNAseq data with multiple treatment groups and each subject has p
... Same design, but this question is from broad perspective, not the detailed question regarding any problem with these packages. For example, what is the most appropriate way to address this question in high dimensional setting. Thanks! ...
written 9 weeks ago by wwu2220
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How to analyze RNAseq data with multiple treatment groups and each subject has pre and post-treatment measures using deseq2/edger/limma?
... Hi, I am working on a set of RNAseq data that has the following design: patients are randomized to different treatment groups: control, trt1 and trt2 each patient has pre and post treatment RNAseq data: time0 , time1 I am interested in getting treatment effect (not time effect). The model mention ...
limma edger deseq2 tutorial written 9 weeks ago by wwu2220 • updated 9 weeks ago by Michael Love23k
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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 4 months 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 4 months 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 4 months 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 4 months 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 4 months 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 4 months ago by wwu2220 • updated 4 months ago by Michael Love23k

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