User: Zhang, Jitao David

Reputation:
80
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Location:
Switzerland
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Google Scholar Page
Last seen:
1 year, 4 months ago
Joined:
4 years, 5 months ago
Email:
j****************@roche.com

Computational biologist working at Roche Innovation Center Basel, F. Hoffmann-La Roche.

Interested in applying statistical and machine learning methods for disease understanding and drug development.

Posts by Zhang, Jitao David

<prev • 14 results • page 1 of 2 • next >
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Comment: C: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Dear Andrea, I looked into the issue and confirm that it's observed in R 3.4 but not in older versions. In case anyone is interested in the cause: the warning is caused by XML::xmlChildren.xmlNode, which tries to build a structure out of NULL in case there's no children of a given XML node. ...
written 9 days ago by Zhang, Jitao David80
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Comment: C: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Dear Andrea, Would you mind providing me the information of sessionInfo()? Because I cannot replicate the findings on my machine, i.e. I did not receive the warnings. My sessionInfo() is as follows: R version 3.3.2 (2016-10-31) > Platform: i686-pc-linux-gnu (32-bit) > Running under: L ...
written 9 days ago by Zhang, Jitao David80
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Answer: A: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Dear Andrea, I will have a look. This should not affect the functionality of the package, though. Best wishes, David On Thu, Jun 8, 2017 at 11:00 AM, AR3513 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User A ...
written 20 days ago by Zhang, Jitao David80
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Answer: A: retrieve human readable gene names from KEGG identifiers
... I am glad that you digged out translateKEGGID2GeneID:) Have fun, David ...
written 16 months ago by Zhang, Jitao David80
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Answer: A: retrieve human readable gene names from KEGG identifiers
... Dear Osvaldo,    Thank you for using KEGGgraph.    The identifier (mmu:12801) is composed of species (mmu) and Entrez Gene ID (12801). So strsplit will do the trick to get EntrezGeneID    From GeneID to gene symbos one can choose many ways. One of them is biomaRt.     Best wishes, David ...
written 16 months ago by Zhang, Jitao David80
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Answer: A: ddCt calculation using bioconductor package
... Dear gv,    From version 1.24.0, it's possible to use a data.frame as input. Check 'example(InputFrame)' out.    Otherwise it's also possible to write a specific parser of eds files. Do you mind sharing an example with me? That can be quite helpful since I do not have access to such files.     If ...
written 2.1 years ago by Zhang, Jitao David80
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segfault in rqubic
... Dear both, It turned out that the problem is caused by the "eset" parameter: it must be an ExpressionSet which has been quantile discretized. The following code worked without error: library(rqubic) NROW <- 2189 NCOL <- 9779 m = matrix(runif(NROW*NCOL, 0, 10), nrow=NROW) ...
microarray cancer rqubic written 3.0 years ago by Zhang, Jitao David80
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Answer: A: segfault in rqubic
... Dear Eric, Thanks for reporting the issue. I will look into it. Do you mind sending me the data that you used so that I could reproduce the errors? Best wishes, David On Sun, May 11, 2014 at 9:13 AM, Eric Liaw [guest] wrote: > Hello, > > I ran into a segfault while trying to run ...
written 3.1 years ago by Zhang, Jitao David80
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Comment: C: Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
... Dear Stuart and Paul, In the latest check-out you can find the KEGGgraph version 1.21.1, where mergeKEGGgraphs accept NULL as list items. In addition the bug identified by Paul in parseKGML2DataFrame in the unit test seems to have been fixed - it was caused by redudant edges in the KGML file an ...
written 3.7 years ago by Zhang, Jitao David80
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Answer: A: Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
... Dear Stuart, The uniqueReaction option has been deleted in the latest release. Could you tell which graph was NULL from AllGraphs? And the KGML file of that? If so I can have a deeper look into the issue. Best, David On Wed, Oct 16, 2013 at 9:50 AM, Stuart Bradley wrote: > Right fi ...
written 3.7 years ago by Zhang, Jitao David80

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