High dimensional data parameters
DATA_FILEMandatory (alternatively with
DATA_FILE_PREFIX). Prefer this to
DATA_FILE_PREFIX. Points to the HD data file.
DATA_FILE_PREFIXdeprecated because it doesn't behave like a prefix (unlike the original pipeline); use
DATA_TYPEMandatory; must be
R(raw values) or
L(log transformed values).
2. If present must be
2. The log base for calculating log values.
SRC_LOG_BASEHas to be specified only with
DATA_TYPE=L. Specifies which logarithm base was used for transforming the data values.
MAP_FILENAMEMandatory. Filename of the mapping file.
Nfor no. Whether the job should be allowed to continue when the data set doesn't provide data for all the annotations (here probes).
Ythen it ignores data points that have no subject mapping. Otherwise (
N) gives an error for such data points.
Ythen the rows with raw values equal 0 would be filtered out. Otherwise (
N) they will be inserted to the database. The flag applies to most of HD data types. It does not effect CNV (ACGH) data. For RNAseq read count data the check on zeros happens based on normalized read count.