The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

User: chris86

gravatar for chris86
chris86380
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

<prev • 163 results • page 1 of 17 • next >
0
votes
1
answer
61
views
1
answer
Highly uneven mapping rates and counts between samples
... 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 ...
normalization limma deseq2 written 16 days ago by chris86380 • updated 16 days ago by Aaron Lun22k
0
votes
1
answer
391
views
1
answers
Answer: A: feature reduction using machine learning
... Your question is not specific enough. Machine learning can mean a great number of things. ...
written 12 weeks ago by chris86380
0
votes
1
answer
345
views
1
answers
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 5 months ago by chris86380
0
votes
0
answers
113
views
0
answers
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 6 months ago by chris86380
0
votes
1
answer
283
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 6 months ago by chris86380
0
votes
2
answers
228
views
2
answers
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 6 months ago by chris86380
0
votes
0
answers
185
views
0
answers
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 6 months ago by chris86380
0
votes
0
answers
185
views
0
answers
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 6 months ago by chris86380
0
votes
0
answers
159
views
0
answers
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 7 months ago by chris86380
1
vote
1
answer
130
views
1
answer
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 8 months ago by chris86380 • updated 8 months ago by Gordon Smyth36k

Latest awards to chris86

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Prior plots from COMBAT
Popular Question 8 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 8 months ago, created a question with more than 1,000 views. For Limma un moderated t-test
Scholar 20 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Popular Question 20 months ago, created a question with more than 1,000 views. For Variance filtering prior to RNA-seq differential expression
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
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
Autobiographer 2.8 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 2.8 years ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 2.8 years ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 2.8 years ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Supporter 2.8 years ago, voted at least 25 times.
Scholar 2.8 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 364 users visited in the last hour