[BioC] LIMMA error: No residual degrees of freedom

[Saurin Jani]

Hi,

Thank you for your reply. My data is generated 24 hrs
of time e.g. (day1)  4 files, (day2)   4 files like
that. 

> design <- model.matrix(~ 0
+factor(c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4));
> colnames(design) <- levels(myRMA$pheno1);

> design
      Group1 Group2 Group3 Group4 
1          1     0     0    0
2          1     0     0    0
3          1     0     0    0
4          1     0     0    0
5          0     1     0    0
6          0     1     0    0
7          0     1     0    0
8          0     1     0    0
9          0     0     1    0
10         0     0     1    0
11         0     0     1    0
12         0     0     1    0
13         0     0     0    1
14         0     0     0    1
15         0     0     0    1
16         0     0     0    1
attr(,"assign")
[1] 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$"factor(c(1, 1, 1, 1, 2, 2, 2, 2,
3, 3, 3, 3, 4, 4, 4, 4))"
[1] "contr.treatment"

I am using Affy kit for over 1 year.

I think as well, my data is highly variable even which
 has only 24 hrs time between them.


Thank you,
Saurin



 


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

> 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
>