User: santos22903

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Posts by santos22903

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viewPathway not showing a gene of interest
... Hi, I was trying to use ReactomePA package to visualize a pathway of interest and a gene of interest. Unfortunately, while the pathway is showing a lot of genes belonging to the pathway, I cannot find mine. I interactively checked it as follows, but the gene is not showing (would be the only one no ...
reactomepa written 4 months ago by santos229030
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Comment: C: Warning in bayes fit in MAST GSEA
... Here it is, after running with 3 bootstrapReplicates: > sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPA ...
written 9 months ago by santos229030
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Warning in bayes fit in MAST GSEA
... Hi, I am trying to do gene set enrichment using MAST. I mostly follow the vignette. Here is the code: gseaFDR <- 0.05 bootstrapReplicates <- 3# 3 for temp testing - takes too long module <- "BTM" # seems, the only one they have anyway packageExt &l ...
gsea mast bayesglm.fit written 9 months ago by santos229030

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