[BioC] Beginner's question: ebayes

[Adaikalavan Ramasamy]

fit2 <- eBayes(fit2)
     ^^^

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Eliana
> Lucchinetti Zaugg
> Sent: 16 March 2004 10:26
> To: Bioconductor Mailing List
> Subject: [BioC] Beginner's question: ebayes
> Importance: High
>
>
> 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
>           lods
>          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
>
> ===============================
> 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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