Can GAGE be used for transcript set pathway analysis
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sun ▴ 100
@sun-5534
Last seen 5.6 years ago
United States
Hello, I have the differential expressed transcript data, e,g TranscriptID Log2FC uc003jmh.1 -7.98049671088886 uc002alj.1 -9.19509271998651 I have converted transcriptIDs to keggEntrezs. uc003jmh.1 hsa04610+730 uc002alj.1 hsa04260+7168 Then I tried to use gage() to get the pathways. It seams the gage() doesn't work (return NA). Can I use gage to do pathway analysis for transcript set? Thank you so much. Rebecca [[alternative HTML version deleted]]
Pathways gage Pathways gage • 915 views
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 10 weeks ago
United States
You would need to convert your transcript ID to gene ID like 730 instead of hsa04610+730 (for uc003jmh.1). Please follow the tutorial and documentation of gage package: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/ gage.pdf http://bioconductor.org/packages/release/bioc/html/gage.html fireflysrb at gmail.com wrote: Hello, I have the differential expressed transcript data, e,g TranscriptID Log2FC uc003jmh.1 -7.98049671088886 uc002alj.1 -9.19509271998651 I have converted transcriptIDs to keggEntrezs. uc003jmh.1 hsa04610+730 uc002alj.1 hsa04260+7168 Then I tried to use gage() to get the pathways. It seams the gage() doesn't work (return NA). Can I use gage to do pathway analysis for transcript set? Thank you so much. Rebecca
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