Nothing
if (interactive()) savehistory();
library("aroma.affymetrix");
log <- Verbose(threshold=-10, timestamp=TRUE);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
chipType <- "HuGene-1_0-st-v1";
footer <- list(
createdOn = format(Sys.time(), "%Y%m%d %H:%M:%S", usetz=TRUE),
createdBy = list(
fullname = "Henrik Bengtsson",
email = sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org")
),
srcFiles = list()
);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Get required annotation files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tags <- ".na31.hg19.transcript";
#tags <- ".na31.hg19.probeset";
pattern <- sprintf("^%s%s([.]|_)(annot[.]|)(csv|CSV)$", chipType, tags);
nax <- AffymetrixNetAffxCsvFile$byChipType(chipType, tags=tags, pattern=pattern);
nbrOfLines(nax); # Count number of lines (once!)
print(nax);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Read data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
data <- readGeneAssignments(nax, verbose=-10);
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