[BioC] LIMMA error: No residual degrees of freedom

[Saurin Jani]

Hi,

If I use more than 4 files for 4 groups..(right now I
am using 16 CEL files, which generated on diff. days
on set of 4), I get zero in Group1-Group2 or any
contrast matrix venn diagram.


contrast.matrix <-
makeContrasts(group4-group1,group3-group1,group2-group1,group4-group2,group3-group2,group4-group3,levels
= design);
fit2 <- contrasts.fit(fit,contrast.matrix);
fit2 <- eBayes(fit2);

results <- decideTests(fit2);

vennDiagram(results);


I get zero in any comparision,Which means my data is
highly variable or something wrong in my design
matrix?

Thank you,
Saurin




--- "James W. MacDonald" <jmacdon at med.umich.edu>
wrote:

> Saurin Jani wrote:
> > Hi ,
> > 
> > I have 4 CEL files and each one is in different
> Group.
> > I am doing ReadAffy() and RMA
> 
> With only one sample per group you cannot fit a
> model because you have 
> no replication (hence, no residual degrees of
> freedom). You will only be 
> able to compute fold changes.
> 
> 
> >  
> > 
> >>pData(myRMA);
> > 
> >      sample   pheno1 pheno2
> > A       1     Group1      1
> > B       2     Group2      2
> > C       3     Group3      3
> > D       4     Group4      4
> > 
> > 
> > 
> >>design <- model.matrix(~ 0 +factor(c(1,2,3,4)));
> >>colnames(design) <-
> > 
> > c("Group1","Group2","Group3","Group4");
> > 
> >>fit <- lmFit(myRMA,design);
> >>contrast.matrix1 <-
> > 
> >
>
makeContrasts(Group2-Group1,Group3-Group4,Group2-Group3,Group4-Group1,Group3-Group1,Group4-Group2,levels
> > = design);
> > 
> >>fitM1 <- contrasts.fit(fit,contrast.matrix1);
> >>fitM1<- eBayes(fitM1);
> > 
> > Error in ebayes(fit = fit, proportion =
> proportion,
> > stdev.coef.lim = stdev.coef.lim) :
> >         No residual degrees of freedom in linear
> model
> > fits
> > 
> > 
> > Any suggestion will be great,
> > 
> > Thank you,
> > Saurin
> > 
> > 
> > 
> > 
> > 		
> > __________________________________ 
> > 
> > The all-new My Yahoo! - What will yours do?
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> -- 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 



		
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