[BioC] LIMMA error: No residual degrees of freedom

[James W. MacDonald]

Saurin Jani wrote:
> 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?

Without seeing the design matrix it is hard to say. However, if 
everything is set up correctly and you don't get any genes, that would 
indicate that none of your fdr-adjusted p-values are less than 0.05. 
This may indicate that your data are highly variable.

You say that the chips were generated on different days. How much time 
elapsed between each chip run? Are we talking weeks or months here? 
Also, did you switch from the Enzo IVT kit to the Affy kit? If so, that 
is a problem too.


> 
> Thank you,
> Saurin
> 

-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109