SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
FPKM is 0, when using cufflinks in galaxy on the net chenyao Bioinformatics 1 12-04-2012 07:12 AM
.NET Bio 1.0 training course rickbe Events / Conferences 0 10-28-2011 09:28 AM
BFAST to Sourceforge.net nilshomer Bioinformatics 9 03-31-2011 10:28 AM

Reply
 
Thread Tools
Old 02-11-2016, 03:14 PM   #1
Anastaziel
Junior Member
 
Location: Moon

Join Date: Jun 2015
Posts: 7
Default A problem with Elastic net + Cox regression

I was trying to perform elastic net + cox regression in R using the glmnet package. The problem is that my data is around 100 individuals with ~100k features and the model is too big for R to store in a matrix. Although the glmnet package can use sparse matrix for the model unfortunately it does not support it with Cox regression.

Anyone knows of another tool I can use (I am not locked in R, it was just the only tool I found)? I read that I can use an SVM (support vector machine) but I still need to calculate the model. I am looking for any tool (R, Matlab, stand alone application) that can perform elastic net + cox regression on a big model. Furthermore, maybe you know how to calculate this big model as a stand alone output so I can use it in an SVM?
Anastaziel is offline   Reply With Quote
Old 02-11-2016, 03:45 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,087
Default

For reference cross-posted: https://www.biostars.org/p/176689/
GenoMax is online now   Reply With Quote
Old 02-11-2016, 03:50 PM   #3
Anastaziel
Junior Member
 
Location: Moon

Join Date: Jun 2015
Posts: 7
Default

I am sorry, I did not know that it is against the rules to post in multiple forums the same question. Not to make another post on this: I will mention if on the other forum the question in answered.

Last edited by Anastaziel; 02-11-2016 at 04:13 PM.
Anastaziel is offline   Reply With Quote
Old 02-11-2016, 03:54 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,087
Default

Quote:
Originally Posted by Anastaziel View Post
I am sorry, I did not know that it is against the rules to post in multiple forums the same question.
No it is not against the rules so don't worry.

I included the link so people can see if your question has been answered on Biostars before they compose a lengthy response (if one was needed) here.

You can help by coming back and posting a closure if your question is answered on Biostars.
GenoMax is online now   Reply With Quote
Old 02-12-2016, 01:53 AM   #5
Anastaziel
Junior Member
 
Location: Moon

Join Date: Jun 2015
Posts: 7
Default

I was able to fix my problem. I was using a wrong test case and my model was becoming too big. Using the example from glment.pdf fixes the issue.
Anastaziel 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 03:56 PM.


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