User: chris86
chris86 • 380
- Reputation:
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- UCL, United Kingdom
- Last seen:
- 2 hours ago
- Joined:
- 2 years, 11 months ago
- Email:
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.
Posts by chris86
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... Hi
I want to implement an ANOVA in ROAST from the limma package? Is this possible? The last thread I found was 4 years old and said it was yet to be included in the package....
I think this would be very useful, I am a big fan of ROAST.
Best wishes,
Chris
...
written 2 days ago by
chris86 • 380
• updated 2 days ago by
Gordon Smyth ♦ 33k
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... If it helps, I don't think there is usually much difference between the two. I use VST because it is a lot faster... personally.
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written 14 days ago by
chris86 • 380
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... It's all in the WGCNA manual I believe, what you are doing.
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written 9 weeks ago by
chris86 • 380
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... Hi
I am just wondering when my package will be updated (M3C) from the development branch which has been more developed than the stable release for a number of months now. There are no build errors atm.
Best wishes,
Chris
...
written 9 weeks ago by
chris86 • 380
• updated 9 weeks ago by
Mike Smith • 2.7k
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... You could just aggregate the gene set genes by their mean, if that makes sense... Then you would be clustering gene sets instead of genes.
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written 3 months ago by
chris86 • 380
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... Hi, sorry, but this isn't much of a question as you have the answer there already.. you would cluster samples using just the gene sets your interested in. Which typically means sub-setting the rows just to contain the genes that are the members of the gene sets you are interested in.
...
written 3 months ago by
chris86 • 380
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... When is expression not meaningful?
We typically filter genes based on an abundance threshold before doing analyses (e.g. a CPM cut off), is this what you mean?
Should you exclude samples based on z-score?
I wouldn't remove samples unless they are clear outliers based on a global gene expression p ...
written 3 months ago by
chris86 • 380
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... Dear bioconductor/ limma developers
I was wondering if there is a straightforward way of getting fold changes per gene set out when I run CAMERA or any of the gene set functions in limma. This is because I need to plot them. I am enjoying using the general pipeline, but at the moment to get the fol ...
written 5 months ago by
chris86 • 380
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