Normalize Plates (Z-Score)

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

x.zscore = (x – mean(x[subset]))/sd(x[subset])
or
x.zscore = (x – median(x[subset]))/mad(x[subset])

Literature: Malo et al., Nat. Biotechnol. 24, 167-179 (2006)
Wikipedia: Z-score / Standard score

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 / well annotation: Select a subset label that is used to calculate mean and sd (median and mad) for each group (e.g. "negative control").
Replace existing values: If checked the raw values will be replaced by the normalized values. Otherwise columns with the normalized values will be appended - ".zscore"
Use robust statistics: Median and mad will be calculated instead of mean and sd.
Column suffix: The default column suffix ".zscore" 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

: Input table

Output Ports

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

Popular Predecessors

Popular Successors

Views

This node has no views

Workflows

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: 2024-11-15

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!