User: chris86
chris86 • 380
- Reputation:
- 380
- Status:
- Trusted
- Location:
- UCL, United Kingdom
- Last seen:
- 1 day, 16 hours ago
- Joined:
- 3 years, 3 months ago
- Email:
- c*************@gmail.com
I am a post-doc data analyst working in Rhuematoid Arthritis research in London.
Posts by chris86
<prev
• 161 results •
page 1 of 17 •
next >
0
votes
1
answers
65
views
1
answers
... 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 22 days ago by
chris86 • 380
0
votes
0
answers
56
views
0
answers
... I think this understanding is correct. So your model would be:
coxph(Surv(OS.month, OS.censor) ~ myvariable, data = x)
...
written 9 weeks ago by
chris86 • 380
0
votes
1
answers
182
views
1
answers
Comment:
C: GSEA for RNA-seq analysis
... I recommend either ROAST (from the limma package) or QuSAGE for gene set analysis.
...
written 9 weeks ago by
chris86 • 380
0
votes
2
answers
118
views
2
answers
... 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 10 weeks ago by
chris86 • 380
0
votes
0
answers
100
views
0
answers
... It is quite straightforward to do w/o the example data, you just need to keep trying.
...
written 11 weeks ago by
chris86 • 380
0
votes
0
answers
100
views
0
answers
... The limma manual is your friend: https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf
...
written 11 weeks ago by
chris86 • 380
0
votes
0
answers
90
views
0
answers
... Probably because it is reordering it internally alphabetically or something like that. You could check the source code.
...
written 3 months ago by
chris86 • 380
1
vote
1
answer
80
views
1
answer
... 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 4 months ago by
chris86 • 380
• updated 4 months ago by
Gordon Smyth ♦ 35k
0
votes
1
answers
136
views
1
answers
... 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 4 months ago by
chris86 • 380
0
votes
1
answers
247
views
1
answers
... It's all in the WGCNA manual I believe, what you are doing.
...
written 6 months ago by
chris86 • 380
Latest awards to chris86
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Limma camera function never gives any differentially expressed gene sets
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Limma un moderated t-test
Scholar
16 months ago,
created an answer that has been accepted.
For A: Heatmap of a subset of genes
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Variance filtering prior to RNA-seq differential expression
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Limma camera function never gives any differentially expressed gene sets
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Prior plots from COMBAT
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Limma camera function never gives any differentially expressed gene sets
Autobiographer
2.4 years ago,
has more than 80 characters in the information field of the user's profile.
Centurion
2.5 years ago,
created 100 posts.
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: Heatmap of a subset of genes
Student
2.5 years ago,
asked a question with at least 3 up-votes.
For Limma camera function never gives any differentially expressed gene sets
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Supporter
2.5 years ago,
voted at least 25 times.
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: Heatmap of a subset of genes
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 200 users visited in the last hour