ChAMP: Error using champ.norm() function
0
0
Entering edit mode
jdangelo • 0
@jdangelo-8953
Last seen 6.0 years ago
United States

Hello, 

I am currently trying to use the ChAMP package in R on a set of 60 samples and have run into a problem with the champ.norm() function. 

I am using ChAMP version 1.4.1 and 64-bit R version 3.1.2 and am using a cluster with 16GB of RAM. 

The error, when running champ.norm() is:

Error in density.default(beta1.v[class1.v == 1]) : 
  need at least 2 points to select a bandwidth automatically
In addition: Warning message:
In max(beta1.v[rand.idx[subsetclass1.v == 1]]) :
  no non-missing arguments to max; returning -Inf

 

I have been looking at other posts to see if this question has been solved but to no avail. Most of the suggestions say to make sure all of my versions are current or memory issues when using too large of a data set, but I have the most recent versions, and am only trying to run ChAMP on 60 samples. 

These are the posts I have looked at:

https://groups.google.com/forum/#!topic/epigenomicsforum/w1ytMQkA3eI

http://stackoverflow.com/questions/28452760/error-in-density-defaultbeta1-vclass1-v-3-need-at-least-2-points-to-se

https://groups.google.com/forum/#!topic/epigenomicsforum/NLeJ32kQrQA

https://groups.google.com/forum/#!msg/epigenomicsforum/w1ytMQkA3eI/L8V5T3ArDgoJ

 

Any help or suggestions would be greatly appreciated.

Best,

Julian

 

ChAMP methylation epigenetics • 993 views
ADD COMMENT

Login before adding your answer.

Traffic: 357 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6