User: Luo Weijun

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Luo Weijun1.4k
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Posts by Luo Weijun

<prev • 207 results • page 1 of 21 • next >
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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 23 days 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 29 days 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 5 weeks 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 10 weeks 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 10 weeks 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 11 weeks 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 12 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 is more likely due to shiny as discussed in the main thread. Note shiny is also loaded in your second sessionInfo. Again the best way is not to load shiny, or use use the pathview web server: https://pathview.uncc.edu/ ...
written 3 months ago by Luo Weijun1.4k
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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 4 months 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 4 months ago by Luo Weijun1.4k

Latest awards to Luo Weijun

Popular Question 6 months ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 3.0 years ago, created an answer that has been accepted. For A: embed url in pathview images
Scholar 3.0 years ago, created an answer that has been accepted. For A: Pathview: Exporting non native KEGG pathway to PNG
Popular Question 3.0 years ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 3.0 years ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Centurion 3.3 years ago, created 100 posts.

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