############################################################################
#
############################################################################
library("aroma.cn.eval");
setOption(aromaSettings, "output/checksum", TRUE);
setOption(aromaSettings, "output/path", FALSE);
setOption(aromaSettings, "output/ram", FALSE);
targetChipType <- chipType;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setting up data sets
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("dsList", mode="list")) {
dsList <- loadAllDataSets(dataSet, chipType=chipType, pattern=sprintf("^%s,.*,pairs", dataSet));
# Set the names
names <- names(dsList);
pattern <- sprintf("^%s(,HCC1143|),", dataSet)
names <- gsub(pattern, "", names);
# CRMA v1
pattern <- "ACC,-XY,CRMAv1(,[-0-9]+|),(AVG|RMA),A[+]B,FLN,-XY,CRMAv1";
gsub(pattern, "CRMAv1,\\2\\1", names);
names <- gsub(pattern, "CRMAv1,\\2\\1", names);
# CRMA v2
pattern <- "ACC,(ra,|)-XY,BPN,-XY(,[-0-9]+|),(AVG|RMA),A[+]B,FLN,-XY";
gsub(pattern, "CRMAv2,\\3\\2", names);
names <- gsub(pattern, "CRMAv2,\\3\\2", names);
pattern <- "ACC,-XY,v1,(AVG|RMA),A[+]B,FLN,-XY";
names <- gsub(pattern, "CRMAv1,\\1", names);
names <- gsub("GTC", "CN5", names);
names <- sapply(names, FUN=strsplit, split=",", fixed=TRUE);
commonTags <- Reduce(intersect, names);
names <- lapply(names, FUN=setdiff, commonTags);
names <- sapply(names, FUN=paste, collapse=",");
names(dsList) <- names;
o <- order(names(dsList));
dsList <- dsList[o];
}
############################################################################
# HISTORY:
# 2009-04-07
# o Generalized to CRMAv1 and CRMAv2.
# 2009-02-23
# o Created.
############################################################################
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