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Question: Can GAGE be used for transcript set pathway analysis
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gravatar for sun
3.5 years ago by
sun100
United States
sun100 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 [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.5 years ago by Luo Weijun1.4k • written 3.5 years ago by sun100
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gravatar for Luo Weijun
3.5 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
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
ADD COMMENTlink written 3.5 years ago by Luo Weijun1.4k
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