0 ×


IBIS Helmholtz-Node extension for KNIME Workbench version 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.


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

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

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


STDOUT and STDERR of the underlying R script.

Best Friends (Incoming)

Best Friends (Outgoing)


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


You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.