## ----eval=FALSE----------------------------------------------------------
## library("GEOquery")
## gse <- getGEO(filename="GSE56761_series_matrix.txt")
## pdata <- pData(gse)[,grepl("characteristics",names(pData(gse)))]


## ----eval=FALSE----------------------------------------------------------
## names(pdata) <- c("strain","treatment","time","replicate")
## pdataclean <- data.frame(strain=ifelse(grepl("wild type",pdata$strain),"wt","mut"),
##                          minute=sub("time  \\(min\\): (.*)","\\1",pdata$time),
##                          replicate=paste0("r",sub("replicate: (.*)","\\1",pdata$replicate)),
##                          row.names=rownames(pdata))
## pdataclean$id <- paste(pdataclean$strain,pdataclean$minute,pdataclean$replicate,sep="_")
## pdataclean$strain <- relevel(pdataclean$strain, "wt")
## pdataclean$minute <- factor(pdataclean$minute, levels=c("0","15","30","60","120","180"))


## ----eval=FALSE----------------------------------------------------------
## load("GSE56761_count_data.Rdata")
## stopifnot(all.equal(rownames(reads.GSE56761), as.character(gene.annotations$pombase_id)))
## colnames(reads.GSE56761) <- tolower(colnames(reads.GSE56761))
## stopifnot(all.equal(colnames(reads.GSE56761), pdataclean$id))
## colnames(reads.GSE56761) <- rownames(pdataclean)
## library("GenomicRanges")
## coldata <- DataFrame(pdataclean)


## ----eval=FALSE----------------------------------------------------------
## genes <- gene.annotations
## rowdata <- GRanges(seqnames=genes$chromosome,
##                    ranges=IRanges(genes$start,
##                      genes$end),
##                    strand=genes$strand,
##                    genes[,6:7])
## rowdata$symbol <- as.character(rowdata$symbol)
## names(rowdata) <- genes$pombase_id


## ----eval=FALSE----------------------------------------------------------
## library("annotate")
## exptdata <- pmid2MIAME("24853205")
## exptdata@url <- "http://www.ncbi.nlm.nih.gov/pubmed/24853205"


## ----eval=FALSE----------------------------------------------------------
## fission <- SummarizedExperiment(SimpleList(counts=reads.GSE56761),
##                                 rowData=rowdata,
##                                 colData=coldata,
##                                 exptData=SimpleList(exptdata))
## save(fission, file="fission.RData")