ConsensusMapNormalizer

Normalizes maps of one consensusXML file

Web Documentation for ConsensusMapNormalizer

Options

version
Version of the tool that generated this parameters file.
algorithm_type
The normalization algorithm that is applied. 'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)
ratio_threshold
Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers.
accession_filter
Use only features with accessions (partially) matching this regular expression for computing the normalization factors. Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used.
description_filter
Use only features with description (partially) matching this regular expression for computing the normalization factors. Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)

Input Ports

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input file [consensusXML]

Output Ports

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output file [consensusXML]

Views

ConsensusMapNormalizer Std Output
The text sent to standard out during the execution of ConsensusMapNormalizer.
ConsensusMapNormalizer Error Output
The text sent to standard error during the execution of ConsensusMapNormalizer. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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