User: AR3513

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AR35130
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Posts by AR3513

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Unable to install Bioconductor packages following R upgrade to 3.5.1
... Thank you very much for your quick reply. I will try that ...
written 10 weeks ago by AR35130
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Unable to install Bioconductor packages following R upgrade to 3.5.1
... Hello,  I've recently upgraded my R version to 3.5.1, and I since them I'm having a lot of problems to install bioconductor packages:  >source("https://bioconductor.org/biocLite.R") >biocLite() Installing package into ‘\\icnas1.cc.ic.ac.uk/hrb08/R/win-library/3.5’ (as ‘lib’ is unspecified) ...
bioclite bioconductor written 10 weeks ago by AR35130 • updated 10 weeks ago by Martin Morgan ♦♦ 22k
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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 6 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 6 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 15 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 15 months ago by AR35130
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Answer: A: legend with gradient in ComplexHeatmap
... Awesome!! Thanks very much !   Andrea ...
written 15 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 15 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 15 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 15 months ago by AR35130

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