[BioC] topTable output ptoblem
Stephen Henderson
s.henderson at ucl.ac.uk
Tue Feb 7 13:31:44 CET 2006
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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