[BioC] topTable output ptoblem

[Stephen Henderson]

Try eBayes(fit2)
Instead of ebayes(fit2)

Does that work?


Stephen Henderson
Wolfson Inst. for Biomedical Research
Cruciform Bldg., Gower Street
University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Assa
Yeroslaviz
Sent: 07 February 2006 09:52
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] topTable output ptoblem

HI;

I've got a problem producing the output of topTable.
My matrix has 2856 rows and 20 columns:
> dim(dataset)
[1] 2856   20

I want to find differential expressed genes between two clusters. For
that
reason i made the design matrix as such:
> cbind(C12=c(rep(1,10), rep(0,10)), C3=c(rep(0,10),rep(1,10)))
      C12 C3
 [1,]   1  0
 [2,]   1  0
 [3,]   1  0
 [4,]   1  0
 [5,]   1  0
 [6,]   1  0
 [7,]   1  0
 [8,]   1  0
 [9,]   1  0
[10,]   1  0
[11,]   0  1
[12,]   0  1
[13,]   0  1
[14,]   0  1
[15,]   0  1
[16,]   0  1
[17,]   0  1
[18,]   0  1
[19,]   0  1
[20,]   0  1

followed by the limma calculations:
>fit <- lmFit(dataset, design)
>cont.matrix<- makeContrasts(C12vsC3=C12-C3, levels=design)
>cont.matrix
    C12vsC3
C12       1
C3       -1
>fit2<- contrasts.fit(fit, cont.matrix)
>fit2 <- ebayes(fit2)

Up to this point I don't get eny problems. Every object has its usual
elements. But when I want to get the topTable of the matrix, I get this
error massage:
> topTable(fit2)
Fehler in array(x, c(length(x), 1), if (!is.null(names(x)))
list(names(x),
:
        Versuch ein Attribut von NULL zu setzen
can anyone please expalin to me what this error is? As far as I know the
columns in the matrix have all the same length and ( I think) they don't
have any NA values

THX,

Assa


--
Assa Yeroslaviz
Loetzener Str. 15
51373 Leverkusen

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