User: Luo Weijun

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Luo Weijun1.4k
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Posts by Luo Weijun

<prev • 194 results • page 1 of 20 • next >
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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 29 days 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 4 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 4 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 5 weeks 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 5 weeks ago by Luo Weijun1.4k
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News: Pathview Web server published in NAR
... The Pathview Web server was recently published in Nucleic Acids Research (NAR) Web Server issue: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx372 Pathview is an R/Bioconductor package for pathway based data integration and visualization. It maps and renders a wide variety of biolo ...
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Answer: A: error when rendering pathway with pathview package
... KEGG made some update to pathway 04723 (both img graph and xml data). In xml data, several bad entries were added as in the example below. Note that the position and size data are obviously wrong (and different from all normal ones), like x="1" y="1" width="1" height="1". This cause the the error in ...
written 7 weeks ago by Luo Weijun1.4k
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Answer: A: GAGE or GSEABase using expression data and pathway.gmt file for mouse
... gage package has a tutorial for data preparation, which described how to use gmt file as gene set data: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/dataPrep.pdf gage can definitely be used for mouse data, please follow the main tutorial: http://bioconductor.org/packages/ ...
written 7 weeks ago by Luo Weijun1.4k
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Answer: A: Pathview: visualization of data
... Michaela, Thanks for your interest in Pathview. Question 1: you can set limit=list(gene=c(0,100), cpd=1) with your pathview() call. Question 2: you need to do pathway analysis to select significantly perturbed pathway first, you may tools like gage: http://bioconductor.org/packages/release/bioc/h ...
written 3 months ago by Luo Weijun1.4k
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Answer: A: Pathview pathview kegg.native=TRUE throws error in img
... Does this error only occur to pathway 04215 or other pathways too, only with this data or other data too? ...
written 3 months ago by Luo Weijun1.4k

Latest awards to Luo Weijun

Popular Question 19 days ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 2.6 years ago, created an answer that has been accepted. For A: embed url in pathview images
Scholar 2.6 years ago, created an answer that has been accepted. For A: Pathview: Exporting non native KEGG pathway to PNG
Popular Question 2.6 years ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 2.6 years ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Centurion 2.8 years ago, created 100 posts.

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