User: Andrew_McDavid
Andrew_McDavid • 190
- Reputation:
- 190
- Status:
- Trusted
- Location:
- Website:
- https://amcdavid.githu...
- Twitter:
- EquivMeasures
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 2 years, 7 months ago
- Email:
- A*************@urmc.rochester.edu
Posts by Andrew_McDavid
<prev
• 37 results •
page 1 of 4 •
next >
1
vote
1
answer
89
views
1
answers
... It's unclear to me what you are trying to accomplish. If you want to test a sequence of responses (even if they aren't gene expression) with the Hurdle model, the easiest way I can see would be to make a SingleCellAssay object. If for some reason you don't want to do that, you could write a for-lo ...
written 6 weeks ago by
Andrew_McDavid • 190
1
vote
1
answer
89
views
1
answers
... Actually you still need to specify `zlm(..., method = 'glm')` to turn off shrinkage in the discrete part. Once you do so, you'll see that the coefficients match exactly. But the residual DOF is still off.
For reasons that are obscure to me at this point (to facilitate "per-term" likelihood ratio ...
written 6 weeks ago by
Andrew_McDavid • 190
1
vote
1
answer
118
views
1
answers
... There are two forms of shrinkage happening, and they were developed after a fair amount of iterative exploration of data at the time, though little of this made it into the paper. One for the logistic regression coefficients, and one for the linear regression $\sigma^2$. In practice, the first on ...
written 6 weeks ago by
Andrew_McDavid • 190
1
vote
1
answer
118
views
1
answers
... Yes, this is possible, and AFAIK is possible in DESeq2, too. It's easy to get tripped up by R builds design matrices from the symbolic formula that contain interactions. When in doubt, expand the interactions explicitly with e.g. `interaction`.
library(MAST)
ng = 10
nc = 20
cd = e ...
written 6 weeks ago by
Andrew_McDavid • 190
0
votes
0
answers
174
views
0
answers
Comment:
C: Warning in bayes fit in MAST GSEA
... Can you provide the output from `sessionInfo()`?
...
written 7 months ago by
Andrew_McDavid • 190
0
votes
0
answers
226
views
0
answers
... Restart R, verify that you are running bioconductor 3.6 with BiocInstaller::biocValid() and make sure you aren't reloading from disk any "stale" objects that were created when you had mismatched package versions. Checking that you can run the equivalent code in the MAITAnalysis vignette should serv ...
written 11 months ago by
Andrew_McDavid • 190
0
votes
0
answers
226
views
0
answers
... Yup. Downgrade MAST to version 1.4.1 (here: http://bioconductor.org/packages/3.6/bioc/html/MAST.html) or upgrade to R 3.5 and Bioconductor 3.7.
...
written 11 months ago by
Andrew_McDavid • 190
0
votes
0
answers
226
views
0
answers
... It looks like you have a mismash of Bioconductor 3.7 and 3.6. What does `BiocInstaller::biocValid()` report? Did you install MAST off of github, or via Bioconductor?
...
written 11 months ago by
Andrew_McDavid • 190
1
vote
1
answer
283
views
1
answers
... Well, if all you care about is the top 10 genes, sure. But you probably will want to know p values and effect sizes, too, which are all in the `datatable.` You can get the top 10 genes by contrast by `order`ing it by contrast and then p value.
...
written 12 months ago by
Andrew_McDavid • 190
1
vote
1
answer
283
views
1
answers
...
If I understood correctly, type1 cells are differentially upregulated in Gene{1,2,7,8}.
The * should represent significance (p < 0.01).
For both the type and cngeneson covaraites as the message at the top of the output states,
the top 4 genes by Z score are showh. The * indicates which contr ...
written 12 months ago by
Andrew_McDavid • 190
Latest awards to Andrew_McDavid
Scholar
11 months ago,
created an answer that has been accepted.
For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
Scholar
11 months ago,
created an answer that has been accepted.
For A: Estimating cell size factors for single cell RNA-seq data
Scholar
24 months ago,
created an answer that has been accepted.
For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
Scholar
24 months ago,
created an answer that has been accepted.
For A: Estimating cell size factors for single cell RNA-seq data
Scholar
24 months ago,
created an answer that has been accepted.
For A: How do you test a contrast in MAST?
Teacher
24 months ago,
created an answer with at least 3 up-votes.
For A: How do you test a contrast in MAST?
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 295 users visited in the last hour