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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@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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}