User: swillis4

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swillis410
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Posts by swillis4

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Comment: C: DESeq2 model design for paired samples with multiple factors
... Thanks. I'll give that model a try. Do you have any advice about whether to try to fit the model with quantitative symbiont data rather than binning as "bleached/unbleached"? ...
written 6 months ago by swillis410
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Comment: A: DESeq2 model design for paired samples with multiple factors
... Thanks for your previous help, Michael.  For whatever reason, the varianceStabilizingTransformation provided a much more informative transformation for the PCA than rlog (to my eye, at least). It revealed that the variation within individuals is much greater than we would have expected, dwarfing any ...
written 6 months ago by swillis410
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Comment: A: DESeq2 model design for paired samples with multiple factors
... Thanks for the quick response, Michael. I can understand that. I suppose I am most concerned if I have specified the model correctly to extract what I am interested in. And more importantly, if the PCA results suggest that the model is not sufficiently accommodating some variance inherent to individ ...
written 6 months ago by swillis410
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DESeq2 model design for paired samples with multiple factors
... I am to the point where the more research I do on paired sample design, the more confused I become, so hopefully I can get some clarification on our design. I am trying to specify the appropriate model in DESeq2 for our RNA-seq data. We have 8 pairs of corals that each came from 3 reefs (1, 3, and ...
rnaseq deseq2 model design written 6 months ago by swillis410

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