User: AR3513

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AR35130
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Posts by AR3513

<prev • 17 results • page 1 of 2 • next >
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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 3 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 3 months ago by AR35130
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Answer: A: legend with gradient in ComplexHeatmap
... Awesome!! Thanks very much !   Andrea ...
written 3 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 3 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 3 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 3 months ago by AR35130
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Answer: A: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Thanks very much! ...
written 3 months ago by AR35130
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Comment: C: KEGGgraph warning: "In structure(x$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 3 months ago by AR35130
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Answer: A: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Thanks very much for your reply. Yes, I know the code is working without problems, but it would be great if you could fix it (if possible) to avoid getting all these warnings. Best wishes,  Andrea   ...
written 4 months ago by AR35130
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KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Hello,  I have been recently getting a warning message with KEGGgraph. See the following example: library(KEGGgraph) library(RCurl) path = "rno00010" file = paste("http://rest.kegg.jp/get/", path, "/kgml", sep = "") pathway = try(getURL(file), silent = TRUE) reactions = try(getReactions(parseKG ...
kegggraph written 4 months ago by AR35130

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