[BioC] Limma error

[Gordon K Smyth]

You must use eBayes() before decideTests(), as in all the documentation examples:

fit <- lmFit(myRMA,design)
fit <- eBayes(fit)
results <- decideTests(fit)

Gordon

> Date: Tue, 14 Dec 2004 08:20:11 -0800 (PST)
> From: Saurin Jani <saurin_jani at yahoo.com>
> Subject: [BioC] Limma error
> To: Bioconductor Bioconductor <bioconductor at stat.math.ethz.ch>
>
> Hi,
>
> I have 12 CEL files and 4 Different groups. 2
> untreated and 2 treated. Can anyone tell me what could
> be wrong with my design matrix. My CEL files are
> highly variable or something? Any answer would be
> helpful.
>
> I have below error :
>
>> results <- decideTests(fit);
> Error in array(x, c(length(x), 1), if
> (!is.null(names(x))) list(names(x),  :
>         attempt to set an attribute on NULL
>
> What I did is:
>
>> treatments <-
> factor(c(1,1,1,2,2,2,3,3,3,4,4,4),labels =
> c("Group1","Group2","Group3","Group4"));
>> contrasts(treatments) <- cbind(comp1 =
> c(1,0,1,0),comp2 = c(1,1,0,0), comp3 = c(0,1,1,0));
>> design <- model.matrix(~treatments);
>> colnames(design) <-
> c("Intersept","G1_G3","G1_G2","G2_G3");
>> design
>    Intersept G1_G3 G1_G2 G2_G3
> 1          1     1     1     0
> 2          1     1     1     0
> 3          1     1     1     0
> 4          1     0     1     1
> 5          1     0     1     1
> 6          1     0     1     1
> 7          1     1     0     1
> 8          1     1     0     1
> 9          1     1     0     1
> 10         1     0     0     0
> 11         1     0     0     0
> 12         1     0     0     0
> attr(,"assign")
> [1] 0 1 1 1
> attr(,"contrasts")
> attr(,"contrasts")$treatments
>        comp1 comp2 comp3
> Group1     1     1     0
> Group2     0     1     1
> Group3     1     0     1
> Group4     0     0     0
>
>> fit <- lmFit(myRMA,design);
>> results <- decideTests(fit);
> Error in array(x, c(length(x), 1), if
> (!is.null(names(x))) list(names(x),  :
>         attempt to set an attribute on NULL
>> vennDiagram(results);
> Error in .class1(object) : Object "results" not found
>
> Thank you,
> Saurin