User: polyptwo

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polyptwo0
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Posts by polyptwo

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Comment: C: What is the biological meaning of genes with FC = 0 after shrinkage
... Yes, I think I will go with s-values as I can relate it to the data that we have and expect, as long as I am able to convince my colleagues (and reviewers) that the approach is a valid in our experimental models. I previously tried to pre-filter these genes, and could get *relatively good* results ...
written 4 days ago by polyptwo0
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Comment: C: What is the biological meaning of genes with FC = 0 after shrinkage
... Thanks Michael for your input. I agree with you in the first section, and I trust more the results from the apeglm shrinkage. However, I am having a hard time with the rest. As one would expect, when applying a certain `lfcTreshold` on the `results()` function (*e.g.* 0.5 for a 1.5 FC, as an extrem ...
written 4 days ago by polyptwo0
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What is the biological meaning of genes with FC = 0 after shrinkage
... Hi, I am analysing an rnaseq with interaction terms that shows extreme values on low count genes. As expected, these genes get shrinked to a FC ≈ 0 with `lfcShrink`. Here are some images of the MA-plot [without](https://imgur.com/KFvuWxr.png) and [with](https://i.imgur.com/0NAZAY5.png) `apeglm` s ...
deseq2 apeglm written 4 days ago by polyptwo0 • updated 4 days ago by Michael Love22k
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Comment: C: DESeq2 Formula Design with two variables and individual normalization
... Thanks for your help! ...
written 10 weeks ago by polyptwo0
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Comment: C: DESeq2 Formula Design with two variables and individual normalization
... Thanks for your response Michael. However, the design `~genotype + stress:treatment` is not possible as the model matrix is not full rank . I guess that I am not fully understanding the linearity here because with my colData (in the original post) I cannot relate to any of the examples on the DESeq ...
written 10 weeks ago by polyptwo0
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DESeq2 Formula Design with two variables and individual normalization
... Formula design We are struggling in understanding the correct design formula for my rnaseq analysis. We have 16 samples, 4 biological replicates with 2 different variables: if they are treated with a drug or not, and if they are stressed or not. We want to know: a) Which is the effect of the treat ...
deseq2 written 10 weeks ago by polyptwo0 • updated 10 weeks ago by Michael Love22k

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