User: chris86

gravatar for chris86
chris86380
Reputation:
380
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Trusted
Location:
UCL, United Kingdom
Last seen:
1 day, 15 hours ago
Joined:
3 years, 4 months ago
Email:
c*************@gmail.com

I am a post-doc data analyst working in Rhuematoid Arthritis research in London.

Posts by chris86

<prev • 162 results • page 1 of 17 • next >
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Answer: A: feature reduction using machine learning
... Your question is not specific enough. Machine learning can mean a great number of things. ...
written 10 days ago by chris86380
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Answer: A: How can I create a mean ROC curve for multiple plotted ROC curves, R
... 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 10 weeks ago by chris86380
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Comment: C: Help with Censoring using the survival package.
... I think this understanding is correct. So your model would be: coxph(Surv(OS.month, OS.censor) ~ myvariable, data = x) ...
written 3 months ago by chris86380
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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 3 months ago by chris86380
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Answer: A: Why do I have this perfect volcano plot from Limma?
... 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 4 months ago by chris86380
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Comment: C: Simple differential expression analysis for 2 groups
... It is quite straightforward to do w/o the example data, you just need to keep trying. ...
written 4 months ago by chris86380
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Comment: C: Simple differential expression analysis for 2 groups
... The limma manual is your friend: https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf ...
written 4 months ago by chris86380
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Comment: C: Dseq2 gives the same results no matter the condition ???
... Probably because it is reordering it internally alphabetically or something like that. You could check the source code. ...
written 5 months ago by chris86380
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ANOVA in ROAST
... 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 ...
limma written 5 months ago by chris86380 • updated 5 months ago by Gordon Smyth35k
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Comment: C: Better to use rlog or vst transformation for data quality assessment of differen
... 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. ...
written 6 months ago by chris86380

Latest awards to chris86

Popular Question 6 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 6 months ago, created a question with more than 1,000 views. For Limma un moderated t-test
Scholar 17 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Variance filtering prior to RNA-seq differential expression
Popular Question 17 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 17 months ago, created a question with more than 1,000 views. For Prior plots from COMBAT
Popular Question 18 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 2.6 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 2.6 years ago, created 100 posts.
Scholar 2.6 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 2.6 years ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 2.6 years ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Supporter 2.6 years ago, voted at least 25 times.
Scholar 2.6 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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