[BioC] Beginner's question: ebayes

Eliana Lucchinetti Zaugg eliana.zaugg at pharma.unizh.ch
Tue Mar 16 11:26:16 MET 2004

Dear all:
I've got 30 chips, 5 controls and 5 chips x5 treatment groups and decided that LIMMA would be the best to analyze these data.
I am using this package for the first time (downloaded and installed today, March 16 2004) and I am thus following the manual instructions. But Alas!
I've got the following error message:

fit2 < eBayes(fit2)
  coefficients stdev.unscaled          sigma    df.residual         method         design      contrasts 
          TRUE           TRUE          FALSE           TRUE          FALSE           TRUE          FALSE 
      df.prior       s2.prior      var.prior     proportion        s2.post              t        p.value 
         FALSE          FALSE          FALSE          FALSE           TRUE           TRUE          FALSE 
Warning message: 
longer object length is not a multiple of shorter object length in: fit2 < eBayes(fit2).

Because of this error, no information is extractable afterwards and obviously I get further error messages:
topTable(fit2,coef=1, adjust="fdr")
Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x),  : 
        attempt to set an attribute on NULL
> clas <-classifyTests(fit2)
Error in classifyTests(fit2) : tstat cannot be extracted from object

Any idea of what went wrong?
Thank you very much for any suggestions!

Eliana Lucchinetti Zaugg, PhD
Institute of Pharmacology and Toxicology 
Section of Cardiovascular Research-Room 17 J 28
University of Zurich
Winterthurerstr. 190
CH-8057 Zürich (Switzerland)
Phone: +41-1-635 59 18
Fax: +41-1-635 68 71
e-mail: eliana.zaugg at pharma.unizh.ch

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