[BioC] Can GAGE be used for transcript set pathway analysis

[Luo Weijun]

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