User: Andrew_McDavid
Andrew_McDavid • 190
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Posts by Andrew_McDavid
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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 10 weeks 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 4 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 4 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 4 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 4 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 10 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 14 months ago by
Andrew_McDavid • 190
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... 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.
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written 14 months ago by
Andrew_McDavid • 190
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... 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 14 months ago by
Andrew_McDavid • 190
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... 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 15 months ago by
Andrew_McDavid • 190
Latest awards to Andrew_McDavid
Scholar
13 months ago,
created an answer that has been accepted.
For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
Scholar
13 months ago,
created an answer that has been accepted.
For A: Estimating cell size factors for single cell RNA-seq data
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Estimating cell size factors for single cell RNA-seq data
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: How do you test a contrast in MAST?
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: How do you test a contrast in MAST?
Scholar
2.3 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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