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Limma

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

This node can find differential expressed genes using the limma package of R. It takes as input a count table and a annotation file.

Options

Method for calculation of normalization factors
Method which is used for calculation of the normalization factors against different library sizes (default: TMM).
Method for CPM normalization
Method which is used for CPM (counts per million) normalization (default: quantile).
P-value correction method
Method which is used for p-value correction against multiple testing (default: BH).

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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Cell 0: ID of feature
Cell 1: Log2 fold change
Cell 2: Average log2 CPM expression
Cell 3: B-statistic
Cell 4: t-statistic
Cell 5: P-value
Cell 6: Adjusted p-value

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

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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