SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error user 31888 Bioinformatics 7 01-29-2016 05:13 PM
RNA-Seq Pathway and Gene-set Analysis Workflows in R/Bioconductor with GAGE/Pathview bigmw Bioinformatics 92 11-17-2015 09:48 AM
Update in the gage RNA-seq pathway analysis joint workflow bigmw Bioinformatics 0 02-12-2014 03:27 PM
Generally Applicable Gene-set Analysis (GAGE) problem wilson90 Bioinformatics 1 08-19-2013 09:28 AM

Reply
 
Thread Tools
Old 02-01-2017, 08:23 AM   #1
Drake
Member
 
Location: Boston

Join Date: Apr 2009
Posts: 10
Default GAGE update and result analysis

Hi,
I have recently started to use gage and I am bit confused about the pathway results data.

1) My pathway results after running gage contain 114 pathways (80 of them are NA); however, when I look online at the KEGG website, I find 120 pathways for my organism. Isn't gage able to use the latest version of online data?

2) My greater and less data contains the same list of pathways .. just in inverse order (but completely different p/q values). However, this is a bit confusing: e.g. my differential expressed gene list does not contain any down-regulated genes for one pathway but only contains genes that are up-regulated in the same pathway. Why do these pathways even appear in the less dataset when there is no single gene down-regulated? Since the p/q values are too high, I will discard the pathway anyways - was just wondering why this is listed. And what's the purpose of listing them if all q-values are similar: e.g. 0.9929488953. In this context, what's a general excepted q-value cut-off when it comes to publishing data? Is 0.2 or even 0.5 still accepted?

3) Are pathways with a set.size lower than 10 not considered in the stats?

Any feedback is appreciated! Thanks
Drake is offline   Reply With Quote
Old 05-16-2017, 05:48 PM   #2
bigmw
Senior Member
 
Location: US

Join Date: Aug 2013
Posts: 123
Default

gage does use the latest data from KEGG if you generate gene set data using kegg.gsets() function. However, the reference pathway list could be out of date. The reason you see NA for 80 pathways is that those pathways are out of the set.size range. In other words, they may have too few genes mapped, hence no gene set test were done on them.
The greater and less elements in the result list correspond to up and down regulation test on all pathways (gene sets), not just the significant ones. You want to go though the gage function documentation for details, something like:
?gage
bigmw is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:53 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO