User: Andrew_McDavid
Andrew_McDavid • 120
- Reputation:
- 120
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- Trusted
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- Website:
- https://amcdavid.githu...
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- EquivMeasures
- Last seen:
- 2 weeks, 4 days ago
- Joined:
- 1 year, 9 months ago
- Email:
- A*************@urmc.rochester.edu
Posts by Andrew_McDavid
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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 5 weeks ago by
Andrew_McDavid • 120
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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 5 weeks ago by
Andrew_McDavid • 120
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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?
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written 5 weeks ago by
Andrew_McDavid • 120
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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.
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written 7 weeks ago by
Andrew_McDavid • 120
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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 7 weeks ago by
Andrew_McDavid • 120
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... The random effects model
lmer.output <- zlm(~ Treatment +(1|Treatment:Plate), data,method='glmer', ebayes=FALSE)
seems like the safer bet. In the fixed effects model, you would probably end up with
an awkward situation where the interactions are significant in some genes and not others, and I do ...
written 8 weeks ago by
Andrew_McDavid • 120
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Comment:
C: Using MAST with DropSeq data
... Technically the issue is the quality of the normality assumption in the continuous portion of the model. In my experience the non-zero component of the log2(1+CPM) has appeared pretty symmetric for droplet technologies, but you could evaluate this yourself informally graphically or formally with t ...
written 11 weeks ago by
Andrew_McDavid • 120
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... The "test" happens in `calcZ`,
which is using the means and variances collected in `gsea@tests`.
The test is nothing fancy, just a normal theory Z-test.
The fancy thing is that the variance collected in `calcZ` consists of a quadratic form on the gene-gene covariance matrix, and that the covari ...
written 12 weeks ago by
Andrew_McDavid • 120
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... In the MAITAnalysis vignette, section 5, a competitive gene set enrichment is performed
zlmCond <- zlm(~condition + cngeneson, sca)
# bootstrap, resampling cells
# R should be set to >50 if you were doing this for real.
boots <- bootVcov1(zlmCond, R=4)
gsea <- gseaAfterBoot(zlmCond, bo ...
written 12 weeks ago by
Andrew_McDavid • 120
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... There is a typo in the arguments to `summary`: `doRLT` should read `doLRT`. No error is triggered because the generic signature includes `...`.
Perhaps the function should check that all of the dot args match and throw an error manually?
...
written 3 months ago by
Andrew_McDavid • 120
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
13 months ago,
created an answer that has been accepted.
For A: How do you test a contrast in MAST?
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: How do you test a contrast in MAST?
Scholar
14 months 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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