User: Luo Weijun

gravatar for Luo Weijun
Luo Weijun1.4k
Reputation:
1,450
Status:
Trusted
Location:
United States
Last seen:
1 day, 12 hours ago
Joined:
11 years, 8 months ago
Email:
l*********@yahoo.com

Posts by Luo Weijun

<prev • 209 results • page 1 of 21 • next >
0
votes
2
answers
87
views
2
answers
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 11 days ago by Luo Weijun1.4k
0
votes
0
answers
54
views
0
answers
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 12 days ago by Luo Weijun1.4k
0
votes
1
answers
127
views
1
answers
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 3 months ago by Luo Weijun1.4k
0
votes
2
answers
211
views
2
answers
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 3 months ago by Luo Weijun1.4k
0
votes
2
answers
183
views
2
answers
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 3 months ago by Luo Weijun1.4k
0
votes
1
answers
375
views
1
answers
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 4 months ago by Luo Weijun1.4k
0
votes
1
answers
144
views
1
answers
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 4 months ago by Luo Weijun1.4k
0
votes
3
answers
280
views
3
answers
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 5 months ago by Luo Weijun1.4k
0
votes
3
answers
280
views
3
answers
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 5 months ago by Luo Weijun1.4k
0
votes
2
answers
409
views
2
answers
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 6 months ago by Luo Weijun1.4k

Latest awards to Luo Weijun

Popular Question 8 months ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 3.2 years ago, created an answer that has been accepted. For A: embed url in pathview images
Scholar 3.2 years ago, created an answer that has been accepted. For A: Pathview: Exporting non native KEGG pathway to PNG
Popular Question 3.2 years ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 3.2 years ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Centurion 3.5 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 141 users visited in the last hour