User: Andrew_McDavid

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Posts by Andrew_McDavid

<prev • 39 results • page 2 of 4 • next >
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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 16 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 16 months ago by Andrew_McDavid190
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Answer: A: MAST: testing differential expression with a nested factorial design
... 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 16 months ago by Andrew_McDavid190
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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 17 months ago by Andrew_McDavid190
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Comment: C: MAST: What does the function gseaAfterBoot do exactly?
... 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 17 months ago by Andrew_McDavid190
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Answer: A: MAST: What does the function gseaAfterBoot do exactly?
... 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 17 months ago by Andrew_McDavid190
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Answer: A: MAST - not getting Hurdle p values
... 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 18 months ago by Andrew_McDavid190
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Comment: C: MAST - not getting Hurdle p values
... What is the output of  summaryCond <- summary(zlmCond, doRLT = TRUE, logFC = TRUE, level = 0.95) table(summaryCond$datatable$component, summaryCond$datatable$contrast, exclude = NULL)   ...
written 18 months ago by Andrew_McDavid190
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Comment: C: MAST - not getting Hurdle p values
... I am unable to replicate.  The vignette compiles fine and summaryCond$datatable contains all the expected components: table(summaryCond$datatable$component) C D H logFC S 6900 6900 2300 4600 6900 Are you trying to adapt the code in the vignette to your own data and it's not working? ...
written 18 months ago by Andrew_McDavid190
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Comment: C: MAST - not getting Hurdle p values
... Are you directly cutting and pasting code from vignette and seeing this issue? ...
written 18 months ago by Andrew_McDavid190

Latest awards to Andrew_McDavid

Scholar 14 months ago, created an answer that has been accepted. For A: MAST reported warning "Coefficients ... are never estimible and will be dropped.
Scholar 14 months ago, created an answer that has been accepted. For A: Estimating cell size factors for single cell RNA-seq data
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.
Scholar 2.3 years ago, created an answer that has been accepted. For A: Estimating cell size factors for single cell RNA-seq data
Scholar 2.3 years ago, created an answer that has been accepted. For A: How do you test a contrast in MAST?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How do you test a contrast in MAST?
Scholar 2.4 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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