User: pierre.marin

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Posts by pierre.marin

<prev • 6 results • page 1 of 1 • next >
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Comment: A: DESeq2 logfoldchange and interaction in model
... Hello, Just thank you I discussed with a statistician collegue and I understand you answers ! So log2foldchange in interaction term for B against A in env 2 is: Log2( (popB.env2/popB.env1) / (popA.env2/popA.env1) ) Thank's ! Juste a question about coding interaction, in the `results vignett ...
written 5 weeks ago by pierre.marin0
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Comment: A: DESeq2 logfoldchange and interaction in model
... Hello , Thank you very much because I understood first I made a mistake because in my model I have interaction and I didn't use the shrinkage function with lfcShrink which seem to be necessary in my case to avoid expression level mistake. ...
written 11 weeks ago by pierre.marin0
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Comment: C: DESeq2 logfoldchange and interaction in model
... Hello, Thank you for the response, I understand better how DESeq2 work. But it remain unclear for me what is taking acount for the folchange calcul when I make a contrast between interactive terms as in my last example. ...
written 11 weeks ago by pierre.marin0
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Comment: C: DESeq2 logfoldchange and interaction in model
... If I understand you, Example with the geneX: Table of normalized mean count for the geneX. G is genotype and T is treatment G T mean G1 T1 0.4578779 G2 T1 203.3252143 G3 T1 1450.3183031 G1 T2 143.0287862 G2 T2 0.0000000 G3 T2 3689.9999219 G1 T3 4 ...
written 11 weeks ago by pierre.marin0
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DESeq2 logfoldchange and interaction in model
... Hello ! PhD student and working with rna-seq data, I used DESeq2 for my analysis but after finishing my work, I believe some elements were misunderstood when using the software. To explain I summarized my model analysis: 3 genotypes (G1,G2,G3) in 3 conditions (T1,T2,T3) and my model: I'm interesting ...
deseq2 R rna-seq logfoldchange written 11 weeks ago by pierre.marin0
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How to properly use and understand chip-seq analysis with DiffBind ?
... Hi everybody ! I'm a PhD student trying to analyse Chip-seq data generated in my project but I'm loosing it to use properly DiffBind package even if I read several times the manual. To illustrate my work : Chip-seq on flies: 3 Lineages (A, B and C) x 3 treatments control included (CT, PQ, CO) ...
diffbind R chip-seq written 10 months ago by pierre.marin0

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