User: Luo Weijun

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Luo Weijun1.4k
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Posts by Luo Weijun

<prev • 210 results • page 1 of 21 • next >
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Answer: A: Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad
... you path.ids2 seems to be all NAs, instead of proper KEGG pathway IDs (like 04130, 00120 etc). That's why these non-existing pathway data files could not be downloaded. you should check why NAs were generated ...
written 12 weeks ago by Luo Weijun1.4k
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Answer: A: Error when installing package gageData
... This is not a gageData specific problem, the installation of other packages failed too in your output. Your code is not consistent with the output either. You code only install gageData, but output shows that other packages were also being installed, and pathview package was loaded somehow. ...
written 3 months ago by Luo Weijun1.4k
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pathview and gage server connection issue
... Dear pathview and gage user,  Recent versions of both packages connect to the Pathview Web server for updated KEGG data. The Pathview server is not accessible in 2/12-2/13. You may experience issues in loading the package or using some functions. Please update your pathview and gage packages to the ...
visualization gage pathview kegg pathway analysis written 3 months ago by Luo Weijun1.4k
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Answer: A: Highlight ECs by KEGG module
... You can definitely visualize/highlight just ECs/genes/nodes from a particular module. In you case, you can do something like: library(pathview) library(KEGGREST) m1=keggLink("ko","M00039") m1=gsub("ko:", "", m1) pv.out <- pathview(gene.data = m1, pathway.id = "00940", out.suffix = "toy.examp ...
written 6 months ago by Luo Weijun1.4k
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Answer: A: Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the
... You may want to update your pathview and Bioconductor to the latest release version. Similar issue was report and solved a few months ago: https://support.bioconductor.org/p/98334/ you may always use pathview web server as an backup when needed: https://pathview.uncc.edu/ HTHs. ...
written 6 months ago by Luo Weijun1.4k
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Answer: A: GAGE after tximport
... GAGE does expect normalized expression data as input. It is essentially a pathway (gene set) level differential expression analysis. Your results make perfect sense. Sometimes, you get many significant pathways, sometimes none. Methods like GAGE or GSEA may select pathway with no individual genes s ...
written 6 months ago by Luo Weijun1.4k
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Answer: A: GAGE: No significant output while it should have
... A few questions: you read the fold changes into the data object. Does data include all genes or just a selected list of differentially expressed genes. GAGE (or similar methods like GSEA) expects all genes included, otherwise, your result would not be good. Is data a 2 column matrix (data.frame), ...
written 7 months ago by Luo Weijun1.4k
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Answer: A: Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
... Gene orders in the data should make no difference in GAGE analysis. You can randomly shuffle the rows in the example datasets (e.g. gse16873) and run GAGE, there will be no difference. It is likely that there are multiple rows corresponding to the same gene IDs in your data. In other case, the orde ...
written 7 months ago by Luo Weijun1.4k
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Answer: A: Pathview -- Error in korg[ridx, coln] : subscript out of bounds
... Thanks for reporting the problem. Indeed, current korg data has a few more columns than the old version. it seems that some old copy of korg data was loaded before you call kegg.species.code(). When you do rm(korg) and then call kegg.species.code(), the updated korg was loaded and it works fine. On ...
written 8 months ago by Luo Weijun1.4k
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Answer: A: Pathview -- Error in korg[ridx, coln] : subscript out of bounds
... I ran the exact same code with pathview_1.16.5 and couldn’t replicate the problem you see. BTW, the demo code in the vignette/tutorial has been fully tested on Bioconductor servers with no error: http://bioconductor.org/checkResults/release/bioc-LATEST/pathview/   I am not sure what happened exa ...
written 8 months ago by Luo Weijun1.4k

Latest awards to Luo Weijun

Popular Question 11 months ago, created a question with more than 1,000 views. For Pathview with non-KEGG organisms?
Popular Question 11 months ago, created a question with more than 1,000 views. For DESeq2 with GAGE
Scholar 11 months ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Scholar 11 months ago, created an answer that has been accepted. For A: embed url in pathview images
Popular Question 11 months ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Popular Question 3.5 years ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 3.5 years ago, created an answer that has been accepted. For A: Pathview: Exporting non native KEGG pathway to PNG
Scholar 3.5 years ago, created an answer that has been accepted. For A: embed url in pathview images
Scholar 3.5 years ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Centurion 3.7 years ago, created 100 posts.

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