User: mforde84

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mforde840
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Posts by mforde84

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Comment: C: [GSVM] bootstrapping error
... thanks for the clarifications. the svn repo is asking for authentication, so ill just wait till the new version gets pushed to bioclite. ...
written 2 days ago by mforde840
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Comment: C: [GSVM] bootstrapping error
... hi robert, unfortunately, the fix didn't work, still getting the same error: > enrichment.scores <- gsva(logCPMrbe.flt, gene.sets, method = "gsva", mx.diff = TRUE, verbose=TRUE, rnaseq=TRUE, no.bootstraps=1000, bootstrap.percent = .632, parallel.sz=8)$es.obs Estimating GSVA scores for 2999 g ...
written 4 days ago by mforde840
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Comment: C: [GSVM] bootstrapping error
... thanks robert. i set parallel.sz to 1 for testing purposes. i think i tried with multiple cores as well, but got a similar error. i might be mistaken though (memory comes and goes). i'll give it a go later in the day with multiple cores, see if that helps. either way, thanks for looking into this ...
written 6 days ago by mforde840
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[GSVM] bootstrapping error
... Hi, I'm trying to run a GSVA analysis with bootstrapping, however it appears that I'm missing some dependancy that I haven't been able to find on google. Sorry for the rudimentary question, but would someone be so kind as to help me find the appropriate package? > enrichment.scores <- gsva(l ...
gsvm bootstrap snow written 6 days ago by mforde840 • updated 6 days ago by Robert Castelo1.8k
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Comment: C: limma -- posthoc analysis when design factor has 3 levels
... Thanks for the help. Martin ...
written 6 days ago by mforde840
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limma -- posthoc analysis when design factor has 3 levels
... Hi, I'm analysing some microarray and rnaseq data for gene set enrichment analysis. I have three independent sample groups. I'm using GSVA to do the enrichment analysis then using limma to fit a model to the GSVA enrichment scores. library(GSVA) library(limma) p <- 10 ## number of genes n <- ...
limma post hoc written 8 days ago by mforde840 • updated 8 days ago by Aaron Lun13k

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