User: AR3513

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AR35130
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Posts by AR3513

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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... Hello,  This is a bit weird because I just tried myself and it's working for me.... Are you sure you have installed and loaded the package? Make sure you haven't missed any of the following steps: ## Install package source("https://bioconductor.org/biocLite.R") biocLite("MetaboSignal") ## Load ...
written 3 months ago by AR35130
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Answer: A: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... Hello,  If you want to build a gene-compound network you can use the package MetaboSignal. See below an script:  library(MetaboSignal) paths_sco = MS_getPathIds(organism_code = "sco") # See all pathways for S.coelicolor metabo_paths_sco = paths_sco[paths_sco[, "Path_type"] == "metabolic", 1] # Ge ...
written 3 months ago by AR35130
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Answer: A: incorrect direction in compound-gene interactions
... Hi,  Thanks very much for your reply. Of course, I understand.  Best wishes,  Andrea ...
written 12 months ago by AR35130
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incorrect direction in compound-gene interactions
... Hello,  I noticed that quite often the gene-compound interactions from the KEGG maps are not retrieved with the right direction when using the function "KEGGpathway2Graph". For example, in  "hsa04930" the D-glucose ("cpd:C00031") interacts with "hsa:5581". This is the direction reported in both the ...
kegggraph written 12 months ago by AR35130
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Answer: A: legend with gradient in ComplexHeatmap
... Awesome!! Thanks very much !   Andrea ...
written 12 months ago by AR35130
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legend with gradient in ComplexHeatmap
... Hello,  I have noticed that the legend for the colors of the heatmaps it has a fix number of breaks (5). Even if I customize the colors myself to include more breaks using colorRamp2, or if I use a continuous scale,  it stills displays only 5 breaks in the legend.  Is there anyway to change the nu ...
complexheatmap written 12 months ago by AR35130
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Answer: A: qvalues lower than pvalues
... Thanks very much for your detailed reply. Really useful. Best wishes,  Andrea ...
written 12 months ago by AR35130
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qvalues lower than pvalues
... Hello,  I have a question regarding the qvalues. I have a dataset of 240 metabolites and I did univariate tests, generating 240 p-values. I then calculated the qvalues from these pvalues, and got few qvalues that are actually lower than the pvalues (e.g. pvalue = 0.07; qvalue = 0.03). I understand ...
qvalue written 12 months ago by AR35130
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Answer: A: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Thanks very much! ...
written 13 months ago by AR35130
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Comment: C: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Thanks very much for your reply. See below: > library(KEGGgraph) Attaching package: ‘KEGGgraph’ The following object is masked from ‘package:graphics’:     plot > library(RCurl) Loading required package: bitops > path = "rno00010" > path = "rno00010" > file = paste("http://rest.k ...
written 13 months ago by AR35130

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