User: Andrew_McDavid

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Posts by Andrew_McDavid

<prev • 23 results • page 1 of 3 • next >
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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 1 day ago by Andrew_McDavid100
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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 1 day ago by Andrew_McDavid100
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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 2 days ago by Andrew_McDavid100
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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 2 days ago by Andrew_McDavid100
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Comment: C: single-cells RNA-seq analysis by MAST with unbalanced group size
... Statistical validity (calibration of p-values) is unaffected by the unbalanced group sizes, but as above, power will be low.  Can you clarify what is meant by "minimal disparity in sample sizes?" ...
written 2 days ago by Andrew_McDavid100
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Answer: A: Using MAST with DropSeq data
... You are right that the native distribution of the UMIs (counts) before doing any normalization is rather distinct from that of qPCR.  After some types of normalization, it's not so different.  We've had good luck by calculating counts per million (or ten thousand, as seem to be popular with 10X dat ...
written 18 days ago by Andrew_McDavid100
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calculateQCmetrics doesn't accept `numeric` `feature_controls` in scater 1.6.2
... Contra the usage example in the "Quality control with scater" vignette, calculateQCmetrics doesn't accept numeric feature_controls: example_sce = calculateQCMetrics(example_sce, feature_controls = 1:40) Error in calculateQCMetrics(example_sce, feature_controls = 1:40) : feature_controls should be ...
scater written 4 weeks ago by Andrew_McDavid100 • updated 29 days ago by Aaron Lun18k
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Answer: A: single-cells RNA-seq analysis by MAST with unbalanced group size
... Statistical validity is unaffected by the unbalanced group sizes.  Just like in an ANOVA or linear regression, the standard error of the estimate will account for the lower precision in the smaller group.  Unbalanced groups does reduce the statistical power, compared to an experiment with balanced g ...
written 7 weeks ago by Andrew_McDavid100
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Comment: C: Differential Expression analysis between distinct scRNA-seq datasets
... This all depends on how you define "batch."  As I understand your design, statistics won't be able to tell you if any differences you see should be ascribed to "treatment" or "plate".  Unless you run some replicates to estimate, or bound, the plate-to-plate variability, these two factors are confoun ...
written 3 months ago by Andrew_McDavid100
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Answer: A: What is the most useful distance measure to use for cell clustering based on MAS
... The L2-norm makes some sense to me, since the residuals may be approximately N(0,1) distributed under a null distribution of exchangeable cells, given the covariates included in the model. The clustering in this case could seen as searching for latent Gaussian structure among the residuals?  The opt ...
written 4 months ago by Andrew_McDavid100

Latest awards to Andrew_McDavid

Scholar 10 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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