User: rfenouil

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rfenouil0
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Posts by rfenouil

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Comment: C: EdgeR blocking and "All combinations of multiple factors"
... Hello James, thank you again for this excellent answer ! I appreciate your effort to explain details, and I'll definitely use this post as reference for future analyses. The example exposed here has been over-simplified so we could focus on the technical details about blocking. As you guessed, G1 ...
written 7 months ago by rfenouil0
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Comment: C: EdgeR blocking and "All combinations of multiple factors"
... Hello James, thank you so much for this comprehensive answer, it helps a lot. About your sentence "But your original design is easier to use and interpret" in answer 3. Do you  suggest that both method can answer similar questions ? I agree that original design is more intuitive but I thought that ...
written 7 months ago by rfenouil0
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EdgeR blocking and "All combinations of multiple factors"
... Dear all, my apologies if this topic has some redundancy with my previous posts but I think this specific question deserves to be treated separately. Previous posts: https://www.biostars.org/p/321516/#321565 https://support.bioconductor.org/p/112953/#112995 I am trying to integrate a differential ...
edger differential gene expression written 7 months ago by rfenouil0 • updated 7 months ago by James W. MacDonald49k
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Comment: C: EdgeR analysis batch effect
... I realized my comment becomes off topic so I created a new post for this specific question. Thank you for your help. ...
written 7 months ago by rfenouil0
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Comment: C: EdgeR analysis batch effect
... Thank you very much for the clear answer. For convenience reasons (automatic analyses), I tend use edgeR in a weird way. The strategy consists in creating a generic design matrix (each combination of conditions makes a column). Then, at the analysis stage, the user can query the fitted model with c ...
written 7 months ago by rfenouil0
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EdgeR analysis batch effect
... Dear all, I analyzed a batch of samples using edgeR in order to isolate differentially expressed genes from a bacteria strain. Two experimental conditions were varying (growing phase and temperature), and I had at least 3 replicates for every set of conditions. We are mostly interested in temperatu ...
edger differential gene expression written 7 months ago by rfenouil0 • updated 7 months ago by Aaron Lun23k

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