Limma

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).

: 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).

: 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

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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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