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Normalize Plates (POC)

HCS-Tools for KNIME version 4.0.0.v202007151505 by Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

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 the mean (or median) is calculated for the selected subset. Based on this estimate, all data points of each group are normalized by applying this formula:

x.poc = x / mean(x[subset]) * 100
or
x.poc = x / median(x[subset]) * 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 / well annotation
Select a subset that is used to calculate mean (median) 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 - ".poc"
Use robust statistics
Median will be calculated instead of mean.
Column suffix
The default column suffix ".poc" 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

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Input table

Output Ports

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Table with normalized values
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Table with statistics used for normalization

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Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.3

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

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