User: Andrew_McDavid

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Posts by Andrew_McDavid

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Logistic regression in MAST - question
... 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_McDavid190
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Answer: A: Logistic regression in MAST - question
... 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_McDavid190
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Comment: C: Estimation of non-trivial contrasts in MAST
... 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_McDavid190
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Answer: A: Estimation of non-trivial contrasts in MAST
... 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_McDavid190
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Comment: C: Warning in bayes fit in MAST GSEA
... Can you provide the output from `sessionInfo()`? ...
written 7 months ago by Andrew_McDavid190
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Comment: C: Error in zlm function model matrix
... 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_McDavid190
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Comment: C: Error in zlm function model matrix
... 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_McDavid190
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Comment: C: Error in zlm function model matrix
... 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_McDavid190
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Comment: C: Interpretation of cngeneson when doing differential expression analysis in MAST
... 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_McDavid190
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Answer: A: Interpretation of cngeneson when doing differential expression analysis in MAST
... 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_McDavid190

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.

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