[BioC] Help with EBAM from siggenes

[Holger Schwender]

Hi Nick,

ebam cannot handle exprSet objects. Try to use

> find.a0(exprs(eset_rma),eset.cl)

This should work.

Best,
Holger



> --- Ursprüngliche Nachricht ---
> Von: "Ettinger, Nicholas" <nicholas-ettinger at uiowa.edu>
> An: <bioconductor at stat.math.ethz.ch>
> Betreff: [BioC] Help with EBAM from siggenes
> Datum: Mon, 26 Dec 2005 10:58:59 -0600
> 
> Hello all!
> 
> I am trying to run some DE analysis on a set of microarry expression
> data.  I have 8 paired chips, 4 with treatment and 4 without treatment.
> 
> When I used the same 'eset_rma' and 'eset.cl' objects with the 'sam'
> function from the siggnes package, they seemed to work fine.  I couldn't
> discern from the siggenes vignette if there were changes that I had to
> make to the .cl file to have EBAM work.  Any suggestions?
> 
> Thanks in advance for any help or suggestions!!
> -Nick
> 
> >pData(eset_rma)
>                 sample
> NE_MDM-INF1.CEL      1
> NE_MDM-INF2.CEL      2
> NE_MDM-INF3.CEL      3
> NE_MDM-INF4.CEL      4
> NE_MDM1.CEL          5
> NE_MDM2.CEL          6
> NE_MDM3.CEL          7
> NE_MDM4.CEL          8
> 
> >eset.cl
> [1]  1  2  3  4 -1 -2 -3 -4
> 
> >find.out <- find.a0(eset_rma, eset.cl)
> EBAM Analysis for the two class paired case.
> 
> Error in xy.coords(x, y) : 'x' and 'y' lengths differ
> In addition: Warning message:
> NaNs produced in: qnorm(p, mean, sd, lower.tail, log.p) 
> Error during wrapup: unable to open connection
> 
> 
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