User: Luo Weijun

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Luo Weijun1.4k
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Posts by Luo Weijun

<prev • 199 results • page 1 of 20 • next >
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Answer: A: Recent build and parsing error in pathview
... pathview is running error-free now: http://bioconductor.org/checkResults/release/bioc-LATEST/pathview/ http://bioconductor.org/packages/release/bioc/html/pathview.html   Thanks to everyone! ...
written 25 days ago by Luo Weijun1.4k
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Answer: A: Recent build and parsing error in pathview
... Thanks David, for the work. Hopefully, it would work this time. Will keep you updated. ...
written 26 days ago by Luo Weijun1.4k
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Answer: A: Multiple samples on the same graph
... You are not calling pathview the right way. In your analysis, you have two fold change vectors from two analyses, i.e. foldchanges and foldchanges2. You should combined them into a single matrix with two columns, say fc.mat, then pass that into argument gene.data, something like: pv.out <- pathv ...
written 27 days ago by Luo Weijun1.4k
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Answer: A: Recent build and parsing error in pathview
... you may always use pathview web server as an backup in case something like this occurred again: https://pathview.uncc.edu/ Pathview Web server provides a intuitive GUI and API to Pathview, a full pathway analysis workflow supporting multiple omics data and integrated analysis, and much more. ...
written 4 weeks ago by Luo Weijun1.4k
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Recent build and parsing error in pathview
... There is a build error showed up with both release and devel version of pathview package since several days ago. And multiple users also complaint on a emerging parsing error (the same issue as the build error) as below:   > library(pathview) > data(gse16873.d) > pv.out <- pathview(g ...
kegggraph gage pathview pathway pathway analysis written 4 weeks ago by Luo Weijun1.4k
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Comment: C: Error in pathview - came out of nowhere without any source code modification
... This seem to be a shiny problem instead of Pathview problem as the R code works well. Sorry I can’t help more as I don’t use shiny. ...
written 12 weeks ago by Luo Weijun1.4k
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Answer: A: Error in pathview - came out of nowhere without any source code modification
... if you have any unknown problem in R, you may also use the pathview web server: https://pathview.uncc.edu/ ...
written 12 weeks ago by Luo Weijun1.4k
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Answer: A: Error in pathview - came out of nowhere without any source code modification
... not sure what’s the problem. I tried your data with the following code, it worked well. Note that pathview() function works with different gene ID types, Entrez, Ensembl Gene, Symbol etc. you don’t need to do ID conversion using bitr() function. inputfile="inputfile.txt" my.data=read.delim(inputfil ...
written 12 weeks ago by Luo Weijun1.4k
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Answer: A: GAGE: no essential member genes for some DE pathways
... Selecting pathways (or gnee sets) based on p-val instead of q-val is not good when there are multiple pathways being tested. Criterion p.val<0.1 makes things even worse. In other words, you select pathways that are not really significant. That’s likely the reason why you don’t see differentially ...
written 3 months ago by Luo Weijun1.4k
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Answer: A: ID unmatched in pathview
... more information is needed to find out your problem. In R, you can do: head(datainv)   what’s the output from above line? ...
written 3 months ago by Luo Weijun1.4k

Latest awards to Luo Weijun

Popular Question 10 weeks ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 2.7 years ago, created an answer that has been accepted. For A: embed url in pathview images
Scholar 2.7 years ago, created an answer that has been accepted. For A: Pathview: Exporting non native KEGG pathway to PNG
Popular Question 2.7 years ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 2.7 years ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Centurion 2.9 years ago, created 100 posts.

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