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

[Mark Robinson]

Hi Martin.

If you set the 'colnames' of design.gain1q BEFORE lmFit, this warning  
(not an error) should go away.

As the warning message says, the contrast rownames don't match the fit 
$coef colnames ... but they would if you set the colnames before  
fitting, right?

Mark


On 11/12/2008, at 9:54 AM, Martin McCabe wrote:

> 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 
> (1,2,1,1,2,2,1,1,2,2,1,1,1,1,1,2,1,1,1,2,1,2,1,2,1,2,1,2,1,1,1,1,1,1 
> )))
>
> {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!
>
> Martin
>
>
> --------------------------------------------
> 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
> Cambridge
> CB2 2QQ
>
> Tel:		01223 762084
> Fax:		01223 586670
> email:	mcm41 at cam.ac.uk
>
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852