Moderator: Kevin Blighe
Kevin Blighe ♦ 69k
- Reputation:
- 69,240
- Status:
- Trusted
- Location:
- Republic of Ireland
- Website:
- https://kevinblighe.co...
- Scholar ID:
- Google Scholar Page
- Last seen:
- an hour ago
- Joined:
- 3 months ago
- Email:
- k**********@outlook.com
Developer / Maintainer of R / Bioconductor packages:
Follow me on:
- Twitter: https://twitter.com/KevinBlighe
- LinkedIn: https://linkedin.com/in/kevinblighe/
- GitHub: https://github.com/kevinblighe
Posts by Kevin Blighe
<prev
• 9,137 results •
page 1 of 914 •
next >
0
votes
1
answer
7.7k
views
1
answers
Comment:
C: GO analysis using topGO
... Thank you - I have made the change ...
written 14 hours ago by
Kevin Blighe ♦ 69k
1
vote
1
answer
4.2k
views
1
answers
... You can filter probes prior to or after normalisation in any microarray analysis pipeline. The above code is generic and it's expected that one adapts this to their own data.
The limma user guide has much more information: https://bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/ ...
written 3 days ago by
Kevin Blighe ♦ 69k
0
votes
1
answer
65
views
1
answers
Comment:
C: Module trait association in wgcna
... In my code, `pink_module` would contain the module values returned by WGCNA, with there being 1 value per sample.
Yes, `mydata` would be of the form that you have shown, but also including extra columns for the modules (pink, blue, green, etc) ...
written 3 days ago by
Kevin Blighe ♦ 69k
1
vote
1
answer
65
views
1
answers
... I think that you are doing it correctly. I would use a binary logistic regression model here, something like:
summary(glm(timezone1 ~ pink_module, data = mydata, family = binomial(link = 'logit')))
You can also just perform a numerical correlation:
cor(as.numeric(mydata$pink_module), myda ...
written 3 days ago by
Kevin Blighe ♦ 69k
0
votes
2
answers
83
views
2
answers
... They will usually be left in the dataset, even after normalisation. However, these probes should begin with AFFX or BGP - see here: https://www.biostars.org/p/167209/#273842
...and you should indeed remove these after normalisation. ...
written 3 days ago by
Kevin Blighe ♦ 69k
0
votes
2
answers
83
views
2
answers
...
Yes, predicted genes may not necessarily have yet been assigned an ID by Ensembl, Entrez, HGNC, et cetera.
This probe genuinely has no matches:
require('hgu133plus2.db')
annotLookup <- select(hgu133plus2.db, keys = c('1563061_at'),
columns = c('PROBEID', 'ENSEMBL', 'SYMBOL', 'ENT ...
written 3 days ago by
Kevin Blighe ♦ 69k
0
votes
1
answer
58
views
1
answers
Comment:
C: WGCNA negative values
... Well, there may be the problem. Your data frame is encoded categorically, i.e., as factors. You need to convert it to a data matrix or to keep it as a data frame but with everything encoded numerically. ...
written 4 days ago by
Kevin Blighe ♦ 69k
1
vote
1
answer
55
views
1
answers
Comment:
C: Does GSVA normalize sampleset?
... Yes, I believe some methods result in further normalisation / transformation. This information can [I believe] be read in the manual pages.
Thank you for posting an answer. ...
written 4 days ago by
Kevin Blighe ♦ 69k
1
vote
2
answers
62
views
2
answers
... Just adding an alternative answer for others:
samtools tview
Kevin
...
written 4 days ago by
Kevin Blighe ♦ 69k
0
votes
1
answer
47
views
1
answers
... Oh, I see what you mean. Do you have a sample of the input data that you've got? ...
written 4 days ago by
Kevin Blighe ♦ 69k
Latest awards to Kevin Blighe
Teacher
17 hours ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Appreciated
3 days ago,
created a post with more than 5 votes.
For EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
Appreciated
4 days ago,
created a post with more than 5 votes.
For A simple tutorial for a complex ComplexHeatmap
Appreciated
6 days ago,
created a post with more than 5 votes.
For A simple tutorial for a complex ComplexHeatmap
Scholar
6 days ago,
created an answer that has been accepted.
For A: How do I subset VCF based on genotype?
Teacher
8 days ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Scholar
8 days ago,
created an answer that has been accepted.
For A: How do I subset VCF based on genotype?
Good Answer
12 days ago,
created an answer that was upvoted at least 5 times.
For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher
12 days ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Good Answer
20 days ago,
created an answer that was upvoted at least 5 times.
For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher
21 days ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Teacher
22 days ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Good Answer
23 days ago,
created an answer that was upvoted at least 5 times.
For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher
24 days ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Scholar
24 days ago,
created an answer that has been accepted.
For A: How to Interpret p-value from multi-curve Kaplan-Meier Graph
Scholar
24 days ago,
created an answer that has been accepted.
For A: How do I subset VCF based on genotype?
Teacher
25 days ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Scholar
25 days ago,
created an answer that has been accepted.
For A: How do I subset VCF based on genotype?
Appreciated
25 days ago,
created a post with more than 5 votes.
For Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
Scholar
28 days ago,
created an answer that has been accepted.
For A: How do I subset VCF based on genotype?
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: How do I subset VCF based on genotype?
Appreciated
5 weeks ago,
created a post with more than 5 votes.
For Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
Good Answer
5 weeks ago,
created an answer that was upvoted at least 5 times.
For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: problem in generating correlation heatmap with significance level
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2130 users visited in the last hour