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 5 weeks 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 5 weeks ago by AR35130
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Answer: A: legend with gradient in ComplexHeatmap
... Awesome!! Thanks very much !   Andrea ...
written 5 weeks 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 5 weeks 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 7 weeks 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 7 weeks ago by AR35130
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Answer: A: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Thanks very much! ...
written 8 weeks ago by AR35130
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Comment: C: KEGGgraph warning: "In structure(x$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 8 weeks ago by AR35130
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Answer: A: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Thanks very much for your reply. Yes, I know the code is working without problems, but it would be great if you could fix it (if possible) to avoid getting all these warnings. Best wishes,  Andrea   ...
written 10 weeks ago by AR35130
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KEGGgraph warning: "In structure(x$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 10 weeks ago by AR35130

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