User: Jon Manning

gravatar for Jon Manning
Jon Manning40
Reputation:
40
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New User
Location:
United Kingdom
Last seen:
1 year, 9 months ago
Joined:
8 years, 7 months ago
Email:
j*******@staffmail.ed.ac.uk

Posts by Jon Manning

<prev • 6 results • page 1 of 1 • next >
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RnBeads and technical replicates in differential analysis
... Hi all, If I define technical replication using the 'replicate.id.column' option in RnBeads, I get some helpful plots in the exploratory analysis. But I can't tell: are these modelled properly in the differential analysis ('a la' duplicateCorrelation in Limma), or should I deal with them myself? On ...
replicates rnbeads written 2.0 years ago by Jon Manning40 • updated 2.0 years ago by rnbeads0
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Comment: C: Do the outputs of Limma's competitive gene set methods (camera, romer) require a
... Thank you for your reply ...
written 2.2 years ago by Jon Manning40
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Comment: C: Do the outputs of Limma's competitive gene set methods (camera, romer) require a
... Thank you for the informative reply. I was confused by the inconsistency of baked-in multiple testing corrections across these methods and thought there might be a reason, but I'm grateful for the clarification. ...
written 2.2 years ago by Jon Manning40
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Update to MSigDB derivates for romer()?
... The files quoted in the romer() manual at http://bioinf.wehi.edu.au/software/MSigDB/ are very helpful, but out of step with the current v5 of MSigDB. Are there plans to update them, or should I crack on and make my own? Many thanks, Jon ...
limma msigdb romer written 2.2 years ago by Jon Manning40 • updated 2.2 years ago by James W. MacDonald45k
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Do the outputs of Limma's competitive gene set methods (camera, romer) require a mutliple testing correction?
... I've been exploring Limma's excellent gene set methods (many thanks to the developers), and I think that romer() is probably what I want to use. I'm only just getting to grips on all the methods and their differences. I suspect that romer() doesn't provide multiple-testing adjustment parameters bec ...
limma romer written 2.2 years ago by Jon Manning40 • updated 2.2 years ago by Gordon Smyth32k
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How to determine if clinical variables are responsible for gene expression with limma
... Hello, I'm new to the Bioconductor list, and fairly new to Bioconductor itself, so excuse me if the following is a stupid question- I've been looking around the list and documentation for a while without finding my answer. The short version of my question is "What is the most appropriate way to de ...
microarray limma written 8.6 years ago by Jon Manning40

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