FilterLowExpressed

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

: Row names: IDs of features.
Column headers are the names of the samples.
Cell 0...n: Count of features in the samples.
: 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

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

Popular Predecessors

Popular Successors

Limma100 %

Views

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

Workflows

KNIME4NGS_Test_DiffExpressionKnime4NGS

Developers

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Installation

To use this node in KNIME, install the extension KNIME4NGS from the below update site following our NodePit Product and Node Installation Guide:

v5.2

Plugin provider: IBIS KNIME Team

Plugin version: 1.8.1.201707071203

On NodePit since: 2023-12-06

Last update: 2024-04-19

KNIME versions: Since v3.6

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