Revision 2bf4b7346eb13ff77a90b84e177d83f94f2377d9 authored by petrovich on 29 January 2019, 16:29:30 UTC, committed by Vladislav Kamenev on 04 February 2019, 16:04:05 UTC
1 parent 34b4118
loadGEO.R
#' Load GEO Dataset.
#'
#' \code{loadGEO} returns the file with serialized ExpressionSet using
#' ProtoBuf, parsed from data downloaded from GEO by identifier.
#'
#' @param name String, containing GEO identifier of the dataset.
#' It should start with 'GSE' or 'GDS' and can include exact GPL
#' to annotate dataset, separated with dash ('-') from the identifier.
#'
#' @param type Type of the dataset: 'GSE' or 'GDS'. If not specified,
#' the function will take first three letters
#' of \code{name} variable as type.
#'
#' @return File with ProtoBuf-serialized ExpressionSet-s
#' that were downloaded by this identifier.
#' For GSE-datasets there can be multiple annotations, so in file will be a
#' list mapping name with GPL to ExpressionSet.
#'
#' @examples
#' \dontrun{
#' loadGEO("GSE27112")
#' loadGEO("GDS4922")
#' }
#'
#' @import Biobase
#' @import GEOquery
loadGEO <- function(name, type = NA) {
cacheDir <- getOption("phantasusCacheDir")
if (is.null(cacheDir)) {
cacheDir <- tempdir()
} else if (!dir.exists(cacheDir)) {
dir.create(cacheDir)
}
mirrorPath <- getOption('phantasusMirrorPath')
if (is.null(mirrorPath)) {
mirrorPath <- "https://ftp.ncbi.nlm.nih.gov"
}
ess <- getES(name, type, destdir = cacheDir, mirrorPath = mirrorPath)
files <- list()
for (i in seq_along(ess)) {
assign("es", ess[[i]], envir = parent.frame())
seriesName <- if (!grepl(pattern = "-", name) && length(ess) > 1)
paste0(name, "-", annotation(ess[[i]])) else name
files[[seriesName]] <- writeToList(ess[[i]])
}
f <- tempfile(pattern = "gse", tmpdir = getwd(), fileext = ".bin")
writeBin(protolite::serialize_pb(files), f)
jsonlite::toJSON(basename(f))
}
#' Load ExpressionSet from GEO Datasets
#'
#'\code{getGDS} return the ExpressionSet object corresponding
#' to GEO Dataset identifier.
#'
#' @param name String, containing GEO identifier of the dataset.
#' It should start with 'GSE' or 'GDS' and can include exact GPL
#' to annotate dataset, separated with dash ('-') from the identifier.
#'
#' @param destdir Directory for caching loaded Series and GPL
#' files from GEO database.
#'
#' @param mirrorPath URL string which specifies the source of matrices.
#'
#' @return ExpressionSet object wrapped in list, that was available by given
#' in \code{name} variable GEO identifier.
#'
#' @examples
#' getGDS('GDS4922')
#'
#' @export
getGDS <- function(name, destdir = tempdir(),
mirrorPath = "https://ftp.ncbi.nlm.nih.gov") {
stub <- gsub("\\d{1,3}$", "nnn", name, perl = TRUE)
filename <- sprintf("%s.soft.gz", name)
gdsurl <- "%s/geo/datasets/%s/%s/soft/%s"
gdsDirPath <- "%s/geo/datasets/%s/%s/soft"
destfile <- file.path(sprintf(gdsurl, destdir, stub, name, filename))
fullGEODirPath <- file.path(sprintf(gdsDirPath, destdir, stub, name))
dir.create(fullGEODirPath, showWarnings = FALSE, recursive = TRUE)
infile <- file.exists(destfile)
if (!file.exists(destfile)) {
tempDestFile <- tempfile(paste0(filename, ".load"), tmpdir=fullGEODirPath)
tryCatch({
utils::download.file(sprintf(gdsurl, mirrorPath,
stub, name, filename),
destfile = tempDestFile,
method="libcurl")
file.rename(tempDestFile, destfile)
infile <- TRUE
},
error = function(e) {
file.remove(tempDestFile)
},
warning = function(w) {
file.remove(tempDestFile)
})
} else {
message(paste("Loading from locally found file", destfile))
}
l <- suppressWarnings(getGEO(GEO = name, destdir = fullGEODirPath, AnnotGPL = TRUE))
# extracting all useful information on dataset
table <- methods::slot(l, "dataTable")
# extracting table ID_REF | IDENTIFIER/SAMPLE | SAMPLE1 | ...
data <- Table(table)
columnsMeta <- Columns(table) # phenoData
sampleNames <- as.vector(columnsMeta[["sample"]])
rownames <- as.vector(data[["ID_REF"]])
symbol <- as.vector(data[["IDENTIFIER"]])
data <- data[, sampleNames] # expression data
exprs <- as.matrix(data)
row.names(exprs) <- rownames
row.names(columnsMeta) <- sampleNames
pData <- AnnotatedDataFrame(data.frame(columnsMeta, check.names = FALSE))
fData <- data.frame(id=rownames, symbol=symbol, row.names = rownames, stringsAsFactors = FALSE)
fData <- AnnotatedDataFrame(fData)
mabstract=ifelse(is.null(Meta(l)$description),"",Meta(l)$description)
mpubmedids=ifelse(is.null(Meta(l)$pubmed_id),"",Meta(l)$pubmed_id)
mtitle=ifelse(is.null(Meta(l)$title),"",Meta(l)$title)
list(ExpressionSet(assayData = exprs,
phenoData = pData,
featureData = fData,
experimentData=new("MIAME",
abstract=mabstract,
title=mtitle,
pubMedIds=mpubmedids,
other=Meta(l))))
}
#' Returns list of ARCHS4 hdf5 files with expression data
#' @param cacheDir base directory for cache
#' @return list of .h5 files
getArchs4Files <- function(cacheDir) {
list.files(paste(file.path(cacheDir), 'archs4', sep = .Platform$file.sep), '*.h5', full.names = TRUE)
}
#' Loads expression data from ARCHS4 count files.
#' Only sapmles with counted expression are kept.
#' If es already containts expression data it is returned as is.
#' @param es ExpressionSet from GEO to check for expression in ARCHS4
#' @param archs4_files list of available .h5 files from ARCHS4 project
#' @return either original es or an ExpressionSet with loaded count data from ARCHS4
loadFromARCHS4 <- function(es, archs4_files) {
if (nrow(es) > 0 ) {
return(es)
}
for (destfile in archs4_files) {
samples <- h5read(destfile, "meta/Sample_geo_accession")
sampleIndexes <- match(es$geo_accession,
samples)
if (sum(!is.na(sampleIndexes)) == 0) {
# no needed samples in this file
H5close()
next
}
genes <- as.character(h5read(destfile, "meta/genes"))
expression <- h5read(destfile,
"data/expression",
index=list(seq_len(length(genes)),
stats::na.omit(sampleIndexes)))
rownames(expression) <- genes
colnames(expression) <- colnames(es)[!is.na(sampleIndexes)]
H5close()
es2 <- ExpressionSet(assayData = expression,
phenoData = phenoData(es[, !is.na(sampleIndexes)]),
annotation = annotation(es),
experimentData = experimentData(es)
)
fData(es2) <- cbind(fData(es2), "Gene symbol"=rownames(es2))
return(es2)
}
return(es)
}
filterFeatureAnnotations <- function(es) {
fvarsToKeep <- c()
if ("Gene symbol" %in% fvarLabels(es)) {
fvarsToKeep <- c(fvarsToKeep, "Gene symbol")
} else {
fvarsToKeep <- c(fvarsToKeep, grep("symbol",
fvarLabels(es),
ignore.case = TRUE,
value = TRUE))
}
if ("Gene ID" %in% fvarLabels(es)) {
fvarsToKeep <- c(fvarsToKeep, "Gene ID")
} else if ("ID" %in% fvarLabels(es)) {
fvarsToKeep <- c(fvarsToKeep, "ID")
} else {
fvarsToKeep <- c(fvarsToKeep, grep("entrez",
fvarLabels(es),
ignore.case = TRUE,
value = TRUE))
}
featureData(es) <- featureData(es)[, fvarsToKeep]
if (!any(sapply(fData(es),
function(x) identical(rownames(es), as.character(x))
))) {
fData(es) <- cbind("id"=rownames(es), fData(es))
}
es
}
filterPhenoAnnotations <- function(es) {
phenoData(es) <- phenoData(es)[,
grepl("characteristics",
varLabels(es),
ignore.case = TRUE) |
(varLabels(es) %in% c("title",
"id",
"geo_accession"
))]
chr <- varLabels(es)[grepl("characteristics",
varLabels(es),
ignore.case = TRUE)]
parsePData <- function(old.phenodata) {
old.pdata <- pData(old.phenodata)
labels <- varLabels(old.phenodata)
new.pdata <- as.data.frame(matrix(NA, nrow = nrow(old.pdata), ncol = 0))
for (i in seq_len(ncol(old.pdata))) {
splitted <- strsplit(as.vector(old.pdata[[i]]), ':')
lengths <- sapply(splitted, length)
if (any(lengths != 2 & lengths != 0)) {
new.pdata[[labels[i]]] <- old.pdata[[i]]
} else {
zeros <- which(lengths == 0)
splitted[zeros] <- replicate(length(zeros), list(c(NA, NA)))
newnames <- unique(trimws(take(splitted, 1)))
newnames <- newnames[which(!is.na(newnames))]
for (j in seq_along(newnames)) {
name <- newnames[j]
if (!(name %in% names(new.pdata))) {
new.pdata[[name]] <- replicate(nrow(new.pdata), NA)
}
indices <- which(name == trimws(take(splitted, 1)))
new.pdata[[name]][indices] <- trimws(take(splitted, 2)[indices])
}
}
}
rownames(new.pdata) <- rownames(old.pdata)
AnnotatedDataFrame(new.pdata)
}
if (ncol(es) > 0) {
phenoData(es) <- parsePData(phenoData(es))
}
es
}
#' Load ExpressionSet from GEO Series
#'
#'\code{getGSE} return the ExpressionSet object(s) corresponding
#' to GEO Series Identifier.
#'
#' @param name String, containing GEO identifier of the dataset.
#' It should start with 'GSE' or 'GDS' and can include exact GPL
#' to annotate dataset, separated with dash ('-') from the identifier.
#'
#' @param destdir Directory for caching loaded Series and GPL
#' files from GEO database.
#'
#' @param mirrorPath URL string which specifies the source of matrices.
#'
#' @return List of ExpressionSet objects, that were available by given
#' in \code{name} variable GEO identifier.
#'
#' @examples
#' \dontrun{
#' getGSE('GSE14308', destdir = 'cache')
#' getGSE('GSE27112')
#' }
#' getGSE('GSE53986')
#'
#' @export
#' @import rhdf5
getGSE <- function(name, destdir = tempdir(),
mirrorPath = "https://ftp.ncbi.nlm.nih.gov") {
GEO <- unlist(strsplit(name, "-"))[1]
stub <- gsub("\\d{1,3}$", "nnn", GEO, perl = TRUE)
filename <- sprintf("%s_series_matrix.txt.gz", name)
gseurl <- "%s/geo/series/%s/%s/matrix/%s"
gseDirPath <- "%s/geo/series/%s/%s/matrix"
destfile <- file.path(sprintf(gseurl, destdir, stub, GEO, filename))
fullGEODirPath <- file.path(sprintf(gseDirPath, destdir, stub, GEO))
dir.create(fullGEODirPath, showWarnings = FALSE, recursive = TRUE)
infile <- file.exists(destfile)
if (!file.exists(destfile)) {
tempDestFile <- tempfile(paste0(filename, ".load"), tmpdir=fullGEODirPath)
tryCatch({
utils::download.file(sprintf(gseurl, mirrorPath,
stub, GEO, filename),
destfile = tempDestFile,
method="libcurl")
file.rename(tempDestFile, destfile)
infile <- TRUE
},
error = function(e) {
file.remove(tempDestFile)
},
warning = function(w) {
file.remove(tempDestFile)
})
} else {
message(paste("Loading from locally found file", destfile))
}
if (infile && file.size(destfile) > 0) {
ess <- list(suppressWarnings(getGEO(filename = destfile,destdir = fullGEODirPath, getGPL = FALSE, AnnotGPL = FALSE)))
for (i in seq_len(length(ess))) {
ess[[i]] <- annotateFeatureData(ess[[i]], destdir)
}
} else {
gpls <- fromJSON(checkGPLs(name))
if (length(gpls) == 0) {
stop(paste("Dataset", name, "not found"))
}
if (length(gpls) == 1 && gpls == name) {
stop(paste("Can't download dataset ", name))
}
ess <- list()
for (i in 1:length(gpls)) {
ess[[gpls[[i]]]] <- getGSE(gpls[[i]], destdir = destdir, mirrorPath = mirrorPath)[[1]]
}
return(ess)
}
archs4_files <- getArchs4Files(destdir)
if (length(archs4_files) > 0) {
ess <- lapply(ess, loadFromARCHS4, archs4_files=archs4_files)
}
ess <- lapply(ess, filterFeatureAnnotations)
ess <- lapply(ess, filterPhenoAnnotations)
ess <- lapply(ess, inferCondition)
ess
}
#' Load ExpressionSet by GEO identifier
#'
#'\code{getES} return the ExpressionSet object(s) corresponding
#' to GEO identifier.
#'
#' @param name String, containing GEO identifier of the dataset.
#' It should start with 'GSE' or 'GDS' and can include exact GPL
#' to annotate dataset, separated with dash ('-') from the identifier.
#'
#' @param type Type of the dataset: 'GSE' or 'GDS'. If not specified,
#' the function will take first three letters
#' of \code{name} variable as type.
#'
#' @param destdir Directory for caching loaded Series and GPL
#' files from GEO database.
#'
#' @param mirrorPath URL string which specifies the source of matrices.
#'
#' @return List of ExpressionSet objects, that were available by given
#' in \code{name} variable GEO identifier.
#'
#' @examples
#' \dontrun{
#' getES('GSE14308', type = 'GSE', destdir = 'cache')
#' getES('GSE27112')
#' }
#' getES('GDS4922')
#'
#' @export
getES <- function(name, type = NA, destdir = tempdir(),
mirrorPath = "https://ftp.ncbi.nlm.nih.gov") {
if (is.na(type)) {
type <- substr(name, 1, 3)
}
possibly.cached <- file.path(destdir, paste0(name, ".rda"))
if (file.exists(possibly.cached)) {
load(possibly.cached)
message(paste("Loaded from locally cached parsed file", possibly.cached))
} else {
if (type == "GSE") {
res <- getGSE(name, destdir, mirrorPath)
} else if (type == "GDS") {
res <- getGDS(name, destdir, mirrorPath)
} else {
stop("Incorrect name or type of the dataset")
}
if (length(res) > 1) {
for (i in 1:length(res)) {
ess <- list(res[[i]])
destfile <- file.path(destdir,
paste0(name,
"-",
annotation(res[[i]]),
".rda"))
message(paste("Cached dataset to ", destfile))
save(ess, file = destfile)
}
}
ess <- res
destfile <- file.path(destdir, paste0(name, ".rda"))
message(paste("Cached dataset to ", destfile))
save(ess, file = destfile)
}
ess
}
listCachedESs <- function(destdir) {
res <- list.files(destdir, pattern=".*\\.rda$")
res <- grep("\\.gz\\.rda$", res, invert = TRUE, value = TRUE)
res <- grep("^(GSE|GDS)", res, value = TRUE)
res <- sub("\\.rda$", "", res)
res
}
#' Reparse cached expression sets from GEO.
#'
#' The function should be used on phantasus version updates that change
#' behavior of loading datasets from GEO. It finds all the datasets
#' that were cached and runs `getES` for them again. The function
#' uses cached Series and other files from GEO.
#'
#' @param destdir Directory used for caching loaded Series files from GEO database.
#'
#' @param mirrorPath URL string which specifies the source of matrices.
#'
#' @return vector of previously cached GSE IDs
#'
#' @examples
#' reparseCachedESs(destdir=tempdir())
#'
#' @export
reparseCachedESs <- function(destdir,
mirrorPath = "https://ftp.ncbi.nlm.nih.gov") {
toReparse <- listCachedESs(destdir)
for (name in toReparse) {
message(paste0("Reparsing dataset ", name))
destfile <- file.path(destdir, paste0(name, ".rda"))
bakfile <- paste0(destfile, ".bak")
tryCatch({
file.rename(destfile, bakfile)
getES(name, destdir = destdir, mirrorPath = mirrorPath)
file.remove(bakfile)
}, error = function(e) {
message(paste0("Error occured while reparsing, old file stored as ",
bakfile))
})
}
return(toReparse)
}
#' Check possible annotations for GEO Dataset.
#'
#' \code{checkGPLs} returns GPL-names for
#' the specified GEO identifier.
#'
#' @param name String, containing GEO identifier of the dataset.
#'
#' @return Vector of filenames serialized in JSON format.
#' If there is only one GPL for that dataset, the function will
#' return \code{name}.
#'
#' @examples
#' \dontrun{
#' checkGPLs('GSE27112')
#' checkGPLs('GSE14308')
#' }
checkGPLs <- function(name) {
mirrorPath <- getOption('phantasusMirrorPath')
if (is.null(mirrorPath)) {
mirrorPath <- "https://ftp.ncbi.nlm.nih.gov"
}
cacheDir <- getOption("phantasusCacheDir")
if (is.null(cacheDir)) {
cacheDir <- tempdir()
} else if (!dir.exists(cacheDir)) {
dir.create(cacheDir)
}
type <- substr(name, 1, 3)
assertthat::assert_that( (type == "GDS" || type == "GSE")
&& nchar(name) >= 4)
stub <- gsub("\\d{1,3}$", "nnn", name, perl = TRUE)
gdsurl <- "%s/geo/%s/%s/%s/"
url <- sprintf(gdsurl, mirrorPath,
if (type == "GDS") "datasets" else "series", stub, name)
gpls <- c()
tryCatch({
httr::GET(url)
if (httr::status_code(httr::GET(url)) == 404) {
warning("No such dataset")
return(jsonlite::toJSON(c()))
} else {
if (type == "GDS") {
gpls <- c(name)
} else {
file.names <- GEOquery:::getDirListing(paste0(url, "matrix/"))
file.names <- file.names[grepl(pattern = paste0("^", name),
x = file.names)]
file.names <- unlist(lapply(file.names, function(x) {
paste0(substr(x, 1, regexpr("_", x) - 1))
}))
if (length(file.names) == 1) {
file.names <- c(name)
}
gpls <- file.names
}
return(jsonlite::toJSON(gpls))
}
},
error = function(e) {
message(paste("Problems establishing connection.",
"Trying to find corresponding files in cache."))
files <- list.files(path = cacheDir)
corresponding <- take(sapply(files[grep(x = files,
pattern = paste0(name, "[-_].*(gz|rda)$"))],
FUN = function(x) { strsplit(x, ".", fixed = TRUE) }), 1)
gpls <- unique(take(sapply(corresponding,
FUN = function(x) { strsplit(x, "_") }), 1))
if (length(gpls) == 0) {
warning("No corresponding files were found")
}
return(jsonlite::toJSON(gpls))
})
}
removeRepeatWords <- function(titles) {
titles_without_repeat_words <- titles
repeat_words <- regmatches(titles, regexpr("(?![-+}\\]\\)])(\\W|_)*\\w*$", titles, ignore.case = TRUE, perl = TRUE))
lsuff <- lcSuffix(repeat_words, ignore.case = TRUE)
if ((all(stringr::str_length(lsuff) == stringr::str_length(repeat_words))) & (all(sub("(\\W*|_)*\\w*$", "", titles, ignore.case = TRUE, perl = TRUE) != ""))) {
titles_without_repeat_words <- sub("(?![-+}\\]\\)])(\\W|_)*\\w*$", "", titles, ignore.case = TRUE, perl = TRUE)
}
if (all(grepl("-$", titles_without_repeat_words, ignore.case = TRUE))) titles_without_repeat_words <- sub("-$", "", titles_without_repeat_words, ignore.case = TRUE, perl = TRUE)
return(titles_without_repeat_words)
}
inferConditionImpl <- function(gse_titles) {
inferCondition <- gse_titles
rep_num <- NULL
if ((length(inferCondition) > 40) | (length(inferCondition) < 3))
{
return(list())
} else if (! all(grepl("[A-z]", inferCondition, ignore.case = TRUE)))
{
return(list())
} else if (all(grepl(" vs[. ]{1}", inferCondition)))
{
return(list())
} else
{
lsuff <- lcSuffix(inferCondition)
suff_length <- stringr::str_length(lsuff)
if (suff_length > 1) inferCondition <- stringr::str_sub(inferCondition, 1, -suff_length-1)
if (all(grepl("((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+", inferCondition, ignore.case = TRUE)))
{
sample <- regmatches(inferCondition, regexpr("((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+", inferCondition, ignore.case = TRUE))
rep_num <- regmatches(sample, regexpr("\\d+$", sample))
inferCondition <- sub("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\W|_)*", "", inferCondition, ignore.case = TRUE, perl = TRUE)
}
else if (all(grepl("((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*[A-z]$", inferCondition, ignore.case = TRUE)))
{
sample <- regmatches(inferCondition, regexpr("((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*[A-z]$", inferCondition, ignore.case = TRUE))
rep_num <- regmatches(sample, regexpr("[A-z]$", sample))
inferCondition <- sub("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*[A-z]$", "", inferCondition, ignore.case = TRUE, perl = TRUE)
}
else if (length(unique(sub("[- \\.#_]*\\d+$", "", inferCondition))) == 1) {
return(list())
}
else if (all(grepl("[- \\.#_]*\\d+$", inferCondition)) & (length(unique(regmatches(inferCondition, regexpr("\\d+$", inferCondition)))) > 1))
{
sample <- sub("\\d+$", "", inferCondition)
if (length(unique(regmatches(sample, regexpr("[- \\.#_]$", sample)))) > 1)
{
return(list())
}
else
{
rep_num <- regmatches(inferCondition, regexpr("\\d+$", inferCondition))
inferCondition <- removeRepeatWords(sub("[ \\.#_]*\\d+$", "", inferCondition))
}
}
else return(list())
}
if ((length(rep_num) > 1) & (length(unique(inferCondition)) < length(unique(gse_titles))) & (length(unique(inferCondition)) > 1))
return(list(condition=inferCondition, replicate=rep_num))
else return(list())
}
inferCondition <- function(es) {
newAnnot <- inferConditionImpl(es$title)
if (length(newAnnot) == 2) {
pData(es)$condition <- newAnnot$condition
pData(es)$replicate <- newAnnot$replicate
}
es
}
getGPLAnnotation <- function (GPL, destdir = tempdir()) {
GPL <- toupper(GPL)
stub = gsub('\\d{1,3}$','nnn',GPL,perl=TRUE)
GPLDirPath <- '%s/geo/platforms/%s/%s/annot'
fullGPLDirPath <- file.path(sprintf(GPLDirPath, destdir, stub, GPL))
dir.create(fullGPLDirPath, showWarnings = FALSE, recursive = TRUE)
return(suppressWarnings(getGEO(GPL, destdir = fullGPLDirPath, AnnotGPL = TRUE)))
}
annotateFeatureData <- function (es, destdir = tempdir()) {
platform <- levels(es$platform_id)[1]
platformParsed <- getGPLAnnotation(platform, destdir)
#https://github.com/seandavi/GEOquery/blob/master/R/parseGEO.R#L569
#############################
vmd <- Columns(platformParsed)
dat <- Table(platformParsed)
## GEO uses "TAG" instead of "ID" for SAGE GSE/GPL entries, but it is apparently
## always the first column, so use dat[,1] instead of dat$ID
## The next line deals with the empty GSE
tmpnames=character(0)
if(ncol(dat)>0) {
tmpnames=as.character(dat[,1])
}
## Fixed bug caused by an ID being "NA" in GSE15197, for example
tmpnames[is.na(tmpnames)]="NA"
rownames(dat) <- make.unique(tmpnames)
## Apparently, NCBI GEO uses case-insensitive matching
## between platform IDs and series ID Refs ???
dat <- dat[match(tolower(rownames(es)),tolower(rownames(dat))),]
# Fix possibility of duplicate column names in the
# GPL files; this is prevalent in the Annotation GPLs
rownames(vmd) <- make.unique(colnames(Table(platformParsed)))
colnames(dat) <- rownames(vmd)
##############################
featureData(es) <- new('AnnotatedDataFrame',data=dat,varMetadata=vmd)
es
}
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