Normalize Plates (NPI)

Groups of data (e.g. wells of a plates) are normalized relative to two subsets (e.g. some wells within that plate, e.g. some negative control wells and some positive controls wells). For each group the mean (or median) is calculated for the two selected subsets. Based on these estimates, all data points of each group are normalized by applying this formula:

x.npi = (mean(x[subset{positive}]) - x) / (mean(x[subset{positive}]) - mean(x[subset{negative}])) * 100
or
x.npi = (median(x[subset{positive}]) - x) / (median(x[subset{positive}]) - median(x[subset{negative}])) * 100

Therfore x.npi values resemble the "percentage of inhibition", where the positive subset is defined as 0% and the negative subset as 100%. By swapping the two subsets the definition will be "percentage of activation" and negatives will be set to 0% and positives to 100%.

Literature: Malo et al., Nat. Biotechnol. 24, 167-179 (2006)

Options

Group data by
Select the column to define the groups (e.g. "barcode" for plate-wise normalization). Select >none< for no grouping (e.g. normalization of the whole screen based on all negative controls available).
Normalize
Select the columns with data to be normalized.
Column with reference label
Select the column which contains the label defining the reference subset (e.g. treatment)
Subset / Positive Control
Select a subset (representing maximum activation) that is used to calculate mean (median) for each group
Subset / Negative Control
Select a subset (representing maximum inhibition) that is used to calculate mean (median) for each group
Replace existing values
If checked the raw values will be replaced by the normalized values. Otherwise columns with the normalized values will be appended - ".npi"
Use robust statistics
Median will be calculated instead of mean.
Column suffix
The default column suffix ".npi" can be changed
Load a limited number of columns
If big data tables create memory problems, the number of columns read in memory (subset data) can be restricted. Then, statistic calculation will be done sequential for each set with the given number of columns.

Input Ports

Icon
Input table

Output Ports

Icon
Table with normalized values
Icon
Table with statistics used for normalization

Popular Predecessors

Popular Successors

Views

This node has no views

Workflows

Links

Developers

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.

Installation

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

v5.3

A zipped version of the software site can be downloaded here.

Plugin provider: Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
Plugin version: 5.3.0.v202407011120
On NodePit since: 2024-07-11
Last update: 2024-11-21
KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!