User: chris86
chris86 • 380
- Reputation:
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- UCL, United Kingdom
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- 1 day, 9 hours ago
- Joined:
- 3 years, 1 month ago
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- c*************@gmail.com
I am a post-doc data analyst working in Rhuematoid Arthritis research in London.
Posts by chris86
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... I think this understanding is correct. So your model would be:
coxph(Surv(OS.month, OS.censor) ~ myvariable, data = x)
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written 3 days ago by
chris86 • 380
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Comment:
C: GSEA for RNA-seq analysis
... I recommend either ROAST (from the limma package) or QuSAGE for gene set analysis.
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written 5 days ago by
chris86 • 380
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... I can only assume this is something weird about the data you have acquired as the analysis code looks fine to me at least.
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written 11 days ago by
chris86 • 380
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... It is quite straightforward to do w/o the example data, you just need to keep trying.
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written 17 days ago by
chris86 • 380
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... The limma manual is your friend: https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf
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written 18 days ago by
chris86 • 380
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... Probably because it is reordering it internally alphabetically or something like that. You could check the source code.
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written 6 weeks ago by
chris86 • 380
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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
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written 8 weeks ago by
chris86 • 380
• updated 8 weeks ago by
Gordon Smyth ♦ 34k
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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 10 weeks 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 4 months ago by
chris86 • 380
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For Limma camera function never gives any differentially expressed gene sets
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For Variance filtering prior to RNA-seq differential expression
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