[BioC] Error message when fitting linear model to Affy data

Martin McCabe mcm41 at cam.ac.uk
Wed Dec 10 23:54:35 CET 2008

Hi.  I've been looking at some Affymetrix U133Plus2.0 chip data on a  
series of primary tumours.  I've used the same script with minor  
variations numerous times to compare subsets of tumours but having  
recently upgraded to R2.8.0 and reloaded bioconductor I've started  
getting an error message.  My script is:

 > library(limma)
 > library(affy)
 > design.gain1q=model.matrix(~0+factor(c 

{where design.gain1q describes the tumours with gain of chromosome 1q}

 > fit=lmFit(rmaMBData, design=design.gain1q)
 > colnames(design.gain1q)=c("Normal1q", "Gain1q")
 > contrast.matrix=makeContrasts(Gain1q-Normal1q, levels=design.gain1q)
 > fit2=contrasts.fit(fit, contrast.matrix)

Then I get the message:

Warning message:
In contrasts.fit(fit, contrast.matrix) :
   row names of contrasts don't match col names of coefficients

Remaining code:
 > fit2=eBayes(fit2)
 > results=topTable(fit2, coef=1, adjust="fdr", number=54675)

Should I worry about this?  What does it mean?
Grateful for any help!


Dr. Martin G. McCabe

Cancer Research UK Clinical Research Training Fellow
Cambridge University Department of Pathology
Division of Molecular Histopathology
Box 231
Level 3, Lab Block
Addenbrooke's Hospital
Hills Road

Tel:		01223 762084
Fax:		01223 586670
email:	mcm41 at cam.ac.uk

More information about the Bioconductor mailing list