User: siajunren

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siajunren0
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Posts by siajunren

<prev • 6 results • page 1 of 1 • next >
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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 5 months ago by siajunren0 • updated 5 months ago by Andrew_McDavid90
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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 7 months ago by siajunren0 • updated 7 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 8 months ago by siajunren0
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calcAverage missing from Scater package
... Hi,  calcAverage function is missing from the latest Scater package.  Thanks. ...
scater written 8 months ago by siajunren0 • updated 8 months ago by Aaron Lun18k
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Comment: C: Question on GeneSetCollection in GSEABase
... Thank you for the demonstration of the "by hand" method. However, I like to avoid that if possible. Following your advice that automated gene set construction is only possible for 'primary identifiers', I mapped my symbols to EntrezID and ran the same line but obtained the same error as before. Do ...
written 11 months ago by siajunren0
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Question on GeneSetCollection in GSEABase
... Hi, I have gone through the vignette and parts of the reference manual but I am still stuck. I have a vector of gene symbols, call this vector “Vec”. These are all the genes which expression levels I have measured with RNA-Seq. Subsequently, I want to perform gene set enrichment analysis with GO b ...
gseabase geneset written 12 months ago by siajunren0 • updated 12 months ago by Martin Morgan ♦♦ 21k

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