Institute for Systems Biology
(c) Trey Ideker, October 2000
Go up one level to [Data-Processing Pipeline]
mergeConds [OPTIONS] -out <matrixFile> -conds <mergeFile 1> [<mergeFile 2> ...]
This script merges data from array experiments involving a series of different
conditions or condition comparisons. Data from each condition comparison (e.g.
i vs. ii) is read from a <mergeFile>, as produced by either the SAM or mergeReps
programs. If SAM output files are used, mergeConds takes the revised ratios and
lambda significance values that SAM produces. Otherwise, if mergeReps files are
used, mergeConds takes the average log ratio of the replicate x and y
measurements and does not report a lambda significance value.
COMMAND LINE OPTIONS:
Options are used to select just a subset of genes to include in the matrix
output. These options may be used cumulatively: each places a further
restriction on the genes considered. For each option, a gene is included if
it passes the specified criterion in ONE OR MORE conditions.
-lam <num> Include only those genes with lambda >= <num>
-rat <num> Include only those genes with log ratio >= <num>
-std <num> Include only those genes with log ratio std dev >= <num>
-n <num> Include only those genes represented by at least <num>
samples per condition.