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_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=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     *

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