User: g.e.novakovsky

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Posts by g.e.novakovsky

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DEXseq with technical replicates
... Hi everyone, I want to do differential exon usage analysis with DEXseq. I have 3 affected (2 technical replicates for each individual, so 6 samples total) and 3 unaffected individuals  (also 2 technical reps for each sample, 6 samples overall). My question is how should I take into account technica ...
dexseq written 5 weeks ago by g.e.novakovsky0 • updated 5 weeks ago by Alejandro Reyes1.6k
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Comment: C: What doest this p.value distribution mean?
... Thank you, I will check it ...
written 9 weeks ago by g.e.novakovsky0
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Comment: C: What doest this p.value distribution mean?
... PCA plot is not great either... Zeros are unaffected patients, Ones are affected. PC2 divides them by gender. ...
written 9 weeks ago by g.e.novakovsky0
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What doest this p.value distribution mean?
... Hi everyone, I am doing an RNA-seq analysis with DESeq2. I have 3 patients with disease (affected) and 3 healthy patients (unaffected). After following standard DESeq2 pipeline (as described here), I got my table with results and p.value column. I decided to check the distribution of p.values and h ...
deseq2 pvalue written 9 weeks ago by g.e.novakovsky0 • updated 9 weeks ago by Michael Love19k
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Comment: C: limma RNA-seq analysis of human data
... Thank you for your reply, In RNA-seq how do you usually handle technical replicates? Do you just analyze them independently (like I did here) or should you sum up the raw count from these replicates? According to this question (https://support.bioconductor.org/p/97390/) you should do summation, am ...
written 4 months ago by g.e.novakovsky0
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limma RNA-seq analysis of human data
... Hi, I am trying to analyze human RNA-seq data with limma. I have two conditions: affected by disease and not affected. More concretely, I have mother (VAN012, not affected), father (VAN013, affected), paternal grandma (VAN0092, affected), a kid (VAN011, girl, affected) and two unrelated and not aff ...
limma human heterogenous written 4 months ago by g.e.novakovsky0 • updated 4 months ago by Aaron Lun20k

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