Exonmap and Limma
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@mathieu-parent-3348
Last seen 8.4 years ago
Hi ! *Exonmap* I am having some issues with the installation of package exonmap. I manages to resolve most of them but here is my last one ! I am trying to follow the tutorial but after I connect to the database (>xmapConnect("rat")) and I try to run their basic command (>symbol.to.gene("TP53")) as a test of connectivity, I get the following response: *Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: Table 'rattus_norvegicus_core_52_34u.xref' doesn't exist)* I am using the common server to do this, so R(2.8), Mysql(v?) and the databases are installed remotely and I use them through bash with ssh. *Limma* I did an RMA on my data following the tutorial. I have 4 biological replicates in 2 groups. I would like to run LIMMA on my data instead of a t-test and then continue to the xmap analysis pipeline. Here is the script I ran, took it from exonmap handouts. I didn't change anything, maybe I should ?? I am sorry, this is really basic but I am starting with both linux and R so.. please help me !!! SessionInfo() included below. Error I get: *Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, : attempt to set an attribute on NULL* Thanks a lot in advance all ! Mathieu Parent parent.mathieu@gmail.com McGill University Nosciences and Neurosurgery /// Center for Bioinformatics Limma Script *pairwise <- function(rma.data,group,gp1,gp2,fc=log2(1),p.value=0.001) { pd <- pData(rma.data) grp <- pd[, colnames(pd) == group] c1 <- grp == gp1 c2 <- grp == gp2 design <- as.matrix(cbind(as.numeric(c1),as.numeric(c2))) colnames(design) <- c(gp1,gp2) fit <- lmFit(rma.data,design) ct <- paste(gp1,"-",gp2,sep="") cont.matrix <- makeContrasts(contrasts=ct,levels=design) fit2 <- contrasts.fit(fit,cont.matrix) fit2 <- eBayes(fit2) result <- decideTests(fit2,lfc=fc,p.value=p.value) keep <- result@".Data" != 0 r <- cbind(p.adjust(fit2$"p.value"[keep]),fit2$"coeff"[keep]) rownames(r) <- names(result@".Data"[keep,]) colnames(r) <- c("adj.p.value","fold.change") r } topN <- function(rma.data,N=20,type=c("both","up","down")) { type <- match.arg(type) i <- 1:dim(rma.data)[1] o <- order(rma.data[,2],decreasing=T) i <- i[o] if(type == "both") N <- floor(N/2) u <- i[1:N] d <- i[length(i)- N + 1:N] keep <- switch(type, both=c(u,d), up=u, down=d) x[keep,,drop=FALSE] } r <- pairwise(rma.data,"group","a","b",fc=4) ps.2 <- rownames(r) * SessionInfo *R version 2.8.1 (2008-12-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] limma_2.16.4 exonmap_2.0.03 RMySQL_0.7-3 DBI_0.2-4 [5] RColorBrewer_1.0-2 genefilter_1.22.0 survival_2.34-1 affy_1.20.2 [9] Biobase_2.2.2 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.3 [4] preprocessCore_1.4.0 RSQLite_0.7-1 * [[alternative HTML version deleted]]
limma exonmap limma exonmap • 565 views
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