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)

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.)

Workflows

• 02-PIA_and_quantKNIME Hub
• ConsensusXMLIdentificaitonSplitterKNIME Hub
• Labelfree with Protein QuantificationKNIME Hub
• labelfree_with_protein_quantificationOpenMS
• labelfree_with_protein_quantificationKNIME Hub
• openmsLFQ_iPRG2015OpenMS
• openmsLFQ_iPRG2015KNIME Hub
• Proteomics_LFQOpenMS
• Proteomics_LFQKNIME Hub

Links

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Developers