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FilterLowExpressed

IBIS Helmholtz-Node extension for KNIME Workbench version 1.8.1.201707071203 by IBIS KNIME Team

The FilterLowExpressed node can be used to filter low expressed genes before differential expression analysis.
It takes as input a count table and an annotation file.

Options

Filtering Mode
Specify whether to apply the read cutoff to the average over all samples or individually to each sample.
Minimum read number
Set the minimum number of reads per sample. (default: 10)
Fraction of samples
Set the fraction of samples which must have the minimum read number. (default: 0.5)
Filter both conditions separately
Choose whether the filter criteria should be met in both conditions (e.g. case and control group). (default: true)

Input Ports

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Row names: IDs of features.
Column headers are the names of the samples.
Cell 0...n: Count of features in the samples.
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Row names: Names of the samples as they are named in the count table.
The column header should be named 'condition'.
Cell 0: Condition (should only contain two conditions).

Output Ports

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The output table has the same format as the input count table, but some genes were filtered out based on the settings.

Views

STDOUT / STDERR
STDOUT and STDERR of the underlying R script.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install KNIME4NGS from the following update site:

KNIME 4.3

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Developers

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