User: filippo.martignano

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Posts by filippo.martignano

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Using VST normalized values for "external" single gene analysis
... Hello. I'm dealing with a particular design: Basically I am looking if DNA alterations (in particular focal CNV) affect somehow gene expression. The idea is to look if the deletion of a gene (or a portion of a gene) leads to disregulation of its expression, and I would like to use Deseq2. I made a ...
normalization deseq2 vst written 7 weeks ago by filippo.martignano0 • updated 7 weeks ago by Michael Love25k
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Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
... Hi! I've performed Cox PH regression analysis using variance stabilized counts (produced with VST from Deseq2) obtained with salmon (at the transcript level) as suggested in this post https://support.bioconductor.org/p/103464/. Now, I would like to perform the same analysis at the gene level; acco ...
deseq2 salmon vst tximport cox-regression written 6 months ago by filippo.martignano0 • updated 6 months ago by Michael Love25k

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