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User: chris86
chris86 • 380
- Reputation:
- 380
- Status:
- Trusted
- Location:
- UCL, United Kingdom
- Website:
- https://intobioinforma...
- Last seen:
- 9 hours ago
- Joined:
- 3 years, 7 months ago
- Email:
- c*************@gmail.com
I am a post-doc data analyst working in Rhuematoid Arthritis research in London.
Posts by chris86
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... Hi
I have Illumina mRNA-seq samples where it seems because of low RINs (2-4) in a bunch of them compared to the others, I am getting very widely varying mapping rates (15%-70%) and therefore counts per sample (e.g. 8,000,000 mapped reads vs 40,000,000). Plus I can't really use RIN/mapping rate as a ...
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... Your question is not specific enough.
Machine learning can mean a great number of things.
...
written 12 weeks ago by
chris86 • 380
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... I can give you code for doing a mean ROC with the Caret package. I'd recommend the Caret package for supervised classification in R instead of coding it yourself, it is quick and easy to learn with 100s of algorithms to choose from. This works:
# usage on Caret fit (txfit) object:
#selectedInd ...
written 5 months ago by
chris86 • 380
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... I think this understanding is correct. So your model would be:
coxph(Surv(OS.month, OS.censor) ~ myvariable, data = x)
...
written 6 months 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.
...
written 6 months 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.
...
written 6 months 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.
...
written 6 months 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
...
written 6 months 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.
...
written 7 months 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
...
written 8 months ago by
chris86 • 380
• updated
8 months ago by
Gordon Smyth ♦ 36k
Latest awards to chris86
Popular Question
11 weeks ago,
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For Prior plots from COMBAT
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8 months ago,
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For Limma camera function never gives any differentially expressed gene sets
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8 months ago,
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For Limma un moderated t-test
Scholar
20 months ago,
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For A: Heatmap of a subset of genes
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20 months ago,
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For Variance filtering prior to RNA-seq differential expression
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For Limma camera function never gives any differentially expressed gene sets
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Prior plots from COMBAT
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Limma camera function never gives any differentially expressed gene sets
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2.8 years ago,
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2.8 years ago,
created 100 posts.
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2.8 years ago,
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For A: Heatmap of a subset of genes
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2.8 years ago,
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For Limma camera function never gives any differentially expressed gene sets
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For A: Heatmap of a subset of genes
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