User: fshodan

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fshodan0
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Posts by fshodan

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Comment: C: ggbio won't plot ideogram in R version 3.3.1, ggplot2 version 3.1.0
... I had the same error, but in R version 3.4.4. ...
written 5 days ago by fshodan0
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Comment: C: topGO "invalid argument to unary operator"
... I just thought it should be less rare, because there are many ontologies, and if user imports smth less mainstream than GO, I can imagine this situation can happen with more than 4 genes. Thanks for the help again! ...
written 27 days ago by fshodan0
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Comment: C: topGO "invalid argument to unary operator"
... You mean it's super rare that people get zero hits and therefore the error never popped up before? ...
written 27 days ago by fshodan0
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Comment: C: topGO "invalid argument to unary operator"
... Haha, super lame mistake, and I thought I double checked the code before writing here... Thanks a lot. However, I think the second one still remains, I mean when I reduce number of genes even more: > dput(genesList) structure(c(0.000323467569697372, 1.47828072650949e-05, 9.09536111428312e-06, ...
written 27 days ago by fshodan0
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Comment: C: topGO "invalid argument to unary operator"
... > genesList <- degs$P.Value[1:5] > names(genesList) <- degs$ENTREZID[1:5] > genesList 677818 107985744 102725022 105370787 260294 3.234676e-04 1.478281e-05 9.095361e-06 2.126379e-03 5.187784e-03 > sampleGOdata <- - new("topGOdata", + ...
written 28 days ago by fshodan0
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topGO "invalid argument to unary operator"
... > genesList <- degs$P.Value > names(genesList) <- degs$ENTREZID > sampleGOdata <- - new("topGOdata", + description = "Simple session", ontology = "BP", + allGenes = genesList, geneSel = function(x){x<0.01}, + nod ...
topgo software error written 28 days ago by fshodan0 • updated 28 days ago by James W. MacDonald48k
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Comment: C: How to use brainarray custom cdf with oligo package?
... Dear James, thanks a lot for this answer! ...
written 6 weeks ago by fshodan0
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[netbenchmark] GeneNet method "Error in .local(object, from, to, ...)"
... GeneNet method usage from netbenchmark package sometimes results in error: > library(netbenchmark) > top20 <- netbenchmark(datasources.names = "syntren300", datasets.num=1, experiments = 280) datasource: syntren300 dataset: 1 aracne.wrap c3net.wrap clr.wrap GeneNet.wrap Estimate (local) f ...
netbenchmark written 11 months ago by fshodan0
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[netbenchmark] Get a list of Regulators
... Hi, for the netbenchmark package (https://github.com/Bioconductor-mirror/netbenchmark) is it possible to get a list of regulators for each generated network? Best, Alina. ...
netbenchmark written 11 months ago by fshodan0

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