SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GSEA: None of the gene sets passed the size thresholds id0 Bioinformatics 3 03-08-2017 08:42 AM
Generally Applicable Gene-set Analysis (GAGE) problem wilson90 Bioinformatics 1 08-19-2013 10:28 AM
Creating Gene Sets - CummeRbund SHeaph Bioinformatics 0 01-17-2013 08:56 AM
From Affy probe sets/gene symbols to genomic coordinates? ETHANol Epigenetics 7 10-25-2010 03:13 AM
Programs comparing gene sets 454andSolid Bioinformatics 0 03-16-2010 03:22 AM

Reply
 
Thread Tools
Old 12-02-2013, 10:50 AM   #1
wmseq
Member
 
Location: IL

Join Date: May 2011
Posts: 71
Default problem with extracting special gene sets from kegg gene sets for gage

Hi bigmw,
With your help, I have downloaded the whole pathway gene sets for honey bees from Kegg successfully. However, when I tried to extract the signaling/metabolic pathway using the command given by you, it seems that something was wrong with the command, because I just got a file of 78 bytes.

This is the command I used:
kegg.gs=kg.ame$kg.sets[kg.ame$sigmet.idx]

How can I check if kegg.gs is right?


Thanks a lot!!

Richard

Last edited by wmseq; 12-02-2013 at 11:03 AM.
wmseq is offline   Reply With Quote
Old 12-02-2013, 07:00 PM   #2
bigmw
Senior Member
 
Location: US

Join Date: Aug 2013
Posts: 123
Default

I assume you’ve done the following:
library(gage)
kg.ame=kegg.gsets("ame")

then do:
lapply(kg.ame, head, 3)
lapply(kg.ame, length)

And post the output here.
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 09:20 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO