## ----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")