normexp error
0
0
Entering edit mode
@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia
> Date: Wed, 20 Jul 2005 11:27:38 +0200 > From: "Rani Elkon" <ranel at="" post.tau.ac.il=""> > Subject: [BioC] normexp error > To: <bioconductor at="" stat.math.ethz.ch=""> > > Hi, > > I'm trying to normalize my data using limma's normexp method. The process > fails at some chips giving the error message pasted below. > Does anyone know how this problem can be circumvented? > > (I'm using limma 2.0.2 and R 2.1.1). > > Thanks, > -Rani. > >> dKa.RG.bgCorrect <- backgroundCorrect(dKa.RG, method="normexp", offset=50) > Corrected array 1 > Corrected array 2 > Corrected array 3 > Corrected array 4 > Corrected array 5 > Error in optim(par = c(beta, log(sigma), log(alpha)), fn = normexp.m2loglik, > : > initial value in 'vmmin' is not finite That's a pity. We had hoped we had made this problem very unlikely in recent versions of limma. Try summary( dKa.RG$R[,6] ) summary( dKa.RG$G[,6] ) summary( dKa.RG$Rb[,6] ) summary( dKa.RG$Gb[,6] ) to see if there are any problems with your data. Other than that, I have no suggestions for a work-around at this time. Gordon
limma limma • 651 views
ADD COMMENT

Login before adding your answer.

Traffic: 734 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