User: MBWatson

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MBWatson0
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Posts by MBWatson

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Sort Bioconductor search results?
... I have a very general question- Is it possible to sort Bioconductor search results  by date? I've noticed that the answers in older threads are sometimes no longer relevant due to updates in the packages about which the question was posted. It would be great to see the most recent posts on a search ...
bioconductor search written 2.4 years ago by MBWatson0 • updated 2.4 years ago by James W. MacDonald49k
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report genes in intersection of Venn diagram with topTable?
... Good afternoon, I am analyzing RNA-Seq data generated from an experiment to test the effects of salinity (15ppt, 35ppt, 60ppt) on different populations (BR and SD). My code for reporting the genes differentially expressed in each contrast is working well but I am wondering if topTable can report th ...
rnaseq limma edger toptable venn diagram written 3.8 years ago by MBWatson0 • updated 3.7 years ago by Gordon Smyth36k
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Comment: C: Same number of topTags reported for different contrasts
... Thank you for the response. Your explanation makes perfect sense.  ...
written 4.0 years ago by MBWatson0
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Same number of topTags reported for different contrasts
... Good afternoon, I am using edgeR to find differentially expressed genes among populations (SD and BR) and salinity treatments (15, 35, 60ppt). I have three biological replicates for each treatment. My experimental design matches very closely the example in section 3.2.4 of the (excellent) edgeR use ...
edger design and contrast matrix toptags written 4.0 years ago by MBWatson0 • updated 4.0 years ago by Gordon Smyth36k
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Answer: A: How to specify 'contrast' in glmLRT command when treatments in design matrix are
... Thank you! The answer seems very obvious now so thank you for your patience with my general R inexperience. ...
written 4.0 years ago by MBWatson0
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How to specify 'contrast' in glmLRT command when treatments in design matrix are named with numbers, not letters
... Hello, I am using edgeR to calculate differential gene expression among individuals from two populations (BR and SD) exposed to three salinity treatments (15, 35, 60 ppt), with three biological replicates each (a, b, c) for 18 samples total. When I create my design matrix, my six treatments are nam ...
rnaseq edger glmlrt() written 4.0 years ago by MBWatson0 • updated 4.0 years ago by James W. MacDonald49k

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For report genes in intersection of Venn diagram with topTable?

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