User: g.e.novakovsky

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Posts by g.e.novakovsky

<prev • 7 results • page 1 of 1 • next >
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problem with DeMAND, gene expression matrix input
... Hi, I am using DeMAND in my research, the method asks for expression matrix, but I am confused, what expression units it asks for, raw counts? or normalized values like (RPKM, FPKM or TPM)? or it doesn't matter? Also, how bad is it if I have only 3 samples in treatment and control group for overall ...
gene expression demand written 9 weeks ago by g.e.novakovsky0
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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 6 months ago by g.e.novakovsky0 • updated 6 months 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 7 months 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 7 months 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 7 months ago by g.e.novakovsky0 • updated 7 months ago by Michael Love21k
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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 9 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 9 months ago by g.e.novakovsky0 • updated 9 months ago by Aaron Lun22k

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