User: siajunren

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siajunren0
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Posts by siajunren

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Comment: C: numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
... Just beautiful.I didn't know there's a GOALL keytype. ...
written 9 months ago by siajunren0
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numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
... Hi, The number of genes in a GO geneset determined by goseq is different from what I obtained by querying org.Hs.eg.db. I ran the following: library(goseq) data(genes) pwf.eg=nullp(genes,"hg19","ensGene") GO.wall.eg=goseq(pwf.eg,"hg19","ensGene", test.cats='GO:BP') head(GO.wall.eg,5) It shows t ...
goseq written 9 months ago by siajunren0 • updated 9 months ago by James W. MacDonald50k
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Comment: C: Is number of rotations dependent on number of gene sets in mroast?
... That's true, didn't consider that. Thanks. I indeed was asking a much more basic question. ...
written 9 months ago by siajunren0
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Comment: C: Conditions for using Fry
... I checked and found my df.prior to be 12.21. Would you consider that to be sufficiently large for fry to be a good approximation? ...
written 9 months ago by siajunren0
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Is number of rotations dependent on number of gene sets in mroast?
... When testing more gene sets with mroast, should number of rotations be increased to maintain the accuracy of p values? If I use x number of rotations for testing 1 gene set, should I use perhaps 10x number of rotations for 10 gene sets so that each gene set gets x rotations? This question obviously ...
limma mroast written 9 months ago by siajunren0 • updated 9 months ago by Gordon Smyth37k
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Conditions for using Fry
... What conditions should be fulfilled for Fry to be a good approximation of mroast with infinite rotations? The manual says that the df.prior should be large and set.statistic="mean". What determines the prior degree of freedom of residual variance? I am guessing it is the number of replicates per exp ...
limma mroast fry written 9 months ago by siajunren0 • updated 9 months ago by Gordon Smyth37k
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Comment: C: limma roast syntax and interpretation
... For the last line of your code: roast(e, myIndex, design, contrasts=cont.matrix, nrot=5000) Shouldn't it be "contrast" instead of "contrasts"? And shouldn't the argument be a numerical vector corresponding to the columns of the design matrix instead of a full contrast matrix? ...
written 9 months ago by siajunren0
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Intepretation of Z scores for gene set enrichment analysis in MAST
... I performed zlmfit on a matrix with MAST for 2 populations of cells, A and B, with population A as intercept. Then I run gseaAfterBoot on the zlfit object after performing bootstrapping with bootVcov1. If I get a positive value Z score for a particular gene set, does it mean that genes in this genes ...
gsea scrna mast written 22 months ago by siajunren0 • updated 22 months ago by Andrew_McDavid190
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How does newSCESet calculate expression matrix
... In the Scater package, according to the vignette, newSCESet generates the exprs slot as log2(counts-per-million) using the cpm function from edgeR, with a “prior count” value of 1. However, this is not the case when I checked. library(scater) set.seed(221) y <- matrix(rnbinom(20,size=1,mu=10),5 ...
scater written 24 months ago by siajunren0 • updated 24 months ago by davis90
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Comment: C: calcAverage missing from Scater package
... After updating my R to the latest version, I could run the calcAverage now. Thank you. ...
written 24 months ago by siajunren0

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Popular Question 9 months ago, created a question with more than 1,000 views. For Intepretation of Z scores for gene set enrichment analysis in MAST

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