User: chiayi

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chiayi0
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Posts by chiayi

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Comment: C: Finding genes respond differently to treatment between many genotype comparison
... Gordon,  Thank you for the answer. I'm excited about further understanding edgeR and design matrix. I really appreciate your time and input.    ...
written 17 months ago by chiayi0
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Comment: C: Finding genes respond differently to treatment between many genotype comparison
... Aaron, Thank you so much for the detailed clarification. This certainly helped me better understand the contrast and ANODEV. I really appreciate it! ...
written 17 months ago by chiayi0
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Finding genes respond differently to treatment between many genotype comparison
... Hello, I have an RNA-seq experiment that I would like to analysis using nested design matrix, similar to section 3.5 in the edgeR User's Guide:  > design <- model.matrix(~Disease+Disease:Patient+Disease:Treatment) > colnames(design) [1] "(Intercept)"                      "DiseaseDisease1" ...
edger differential expression nested design written 17 months ago by chiayi0 • updated 17 months ago by Gordon Smyth38k
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signed kME(MM) for finding hub genes in modules of interest
... I found a related but not quite the same quesiton in this post (https://support.bioconductor.org/p/87530/) as mine is specific about findind the hub genes in modules of interest. The hub gene I refer to in this post follows the definition in 7d of this turorial (https://labs.genetics.ucla.edu/horvat ...
wgcna written 2.3 years ago by chiayi0

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