Hi, I am currently trying to use the SPIA bioconductor package and I came across an error that I am not sure how to solve it. I used the contrast.fit method from Limma to obtain a list of significantly differentially expressed genes. Following that, I wanted to use the SPIA package, but it kept on giving me the error : "Error in spia(de = DE_top, all = ALL_top, organism = "hsa", nB = 2000, : de must be a vector of log2 fold changes. The names of de should be included in the refference array!" Would you know what the problem is? The fold change column from the contrast.fit method was not given as logFC, so I changed the names of the columns to FC. Would that be the issue? I have attached the protocol I typed into Bioconductor at the end of this email. Thank you very much for your help. Regards Barbara Bo Ju Shih #### Limma #### f<- factor (targets$GErep, levels=c("1", "2", "3")) reps<-c(1,2,3,4,3, 5, 6,5,7,8,7,9, 10, 9, 11, 12, 13, 14, 15) arraycor<-duplicateCorrelation(exprs(esetPROC), block=reps) design<-model.matrix(~0+f) colnames(design)<-c("TopandMargin", "Middle", "Normal") fit<-lmFit(exprs(esetPROC), design, cor=arraycor$consensus) top_contrast.matrix<-makeContrasts(TopandMargin-Normal, levels= design) top_fit <-contrasts.fit (fit, top_contrast.matrix) top_fit <- eBayes(top_fit) top_TopTable<-topTable(top_fit, number=40000) top<-top_TopTable ### SPIA ### library(SPIA) x <-hgug4112aENTREZID top$ENTREZ <- unlist(as.list(x[top$ID])) top <- top[!is.na(top$ENTREZ), ] tg1 <- top[top$adj.P.Val < 0.05, ] DE_top = tg1$logFC names(DE_top) <- as.vector(tg1$ENTREZ) ALL_top = top$ENTREZ DE_top[1:10] ALL_top[1:10] res = spia(de = DE_top, all = ALL_top, organism = "hsa",nB = 2000, plots = FALSE, beta = NULL) -- Barbara Shih Plastic and Reconstructive Surgery Research (PRSR) Manchester Interdisciplinary Biocentre (MIB) University of Manchester 131 Princess Street Manchester. M1 7DN. United Kingdom University Lab : 0044 161 306 8921 University Fax : 0044 161 306 5177 Email : barbara.b.shih at manchester.ac.uk Website : www.plasticsurgeryresearch.org