User: Andrew_McDavid
Andrew_McDavid • 190
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Posts by Andrew_McDavid
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... There is no minimum a priori, with the following caveats:
1. The tests rely on asymptotic theory to establish the correctness of the p-values. 20 cells may be on the low side. In https://www.ncbi.nlm.nih.gov/pubmed/23267174 we found when the frequency of expression, times the number of cells is ...
written 6 weeks ago by
Andrew_McDavid • 190
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... When I am doing DE test between 10 cells vs another 10 cells, I nearly can't find any DEs. After I increased the number of cells to do DE test ( including above 20 cells), I can get about hundreds of DEGs. So may I ask is there minimum number of cell requirement for MAST? ...
written 6 weeks ago by
Andrew_McDavid • 190
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... If `batch` is indeed crossed with `condition`, as the OP seemed to indicate, this suggests the model of the form
```
~ cluster/condition + batch:cluster
```
where `cluster` is factor that identifies the cluster assignment, derived however desired. You could fit this model in any number of ways, in ...
written 9 weeks ago by
Andrew_McDavid • 190
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... What you wrote seems accurate. If not otherwise specified, eg with `logFC(contrast0 = ...)`, the **coefficient** of your continuous covariate `Cov` will be set to zero, which in this case would mean that `Cov` is equal to zero. This may not be desirable, though it depends on what the covariate is. ...
written 5 months ago by
Andrew_McDavid • 190
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... 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 7 months ago by
Andrew_McDavid • 190
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... 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 7 months ago by
Andrew_McDavid • 190
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... 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 7 months ago by
Andrew_McDavid • 190
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... 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 7 months ago by
Andrew_McDavid • 190
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Comment:
C: Warning in bayes fit in MAST GSEA
... Can you provide the output from `sessionInfo()`?
...
written 13 months ago by
Andrew_McDavid • 190
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... 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 17 months ago by
Andrew_McDavid • 190
Latest awards to Andrew_McDavid
Scholar
16 months ago,
created an answer that has been accepted.
For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
Scholar
16 months ago,
created an answer that has been accepted.
For A: Estimating cell size factors for single cell RNA-seq data
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: Estimating cell size factors for single cell RNA-seq data
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: How do you test a contrast in MAST?
Teacher
2.5 years ago,
created an answer with at least 3 up-votes.
For A: How do you test a contrast in MAST?
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
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