Normalize Plates (POC)

HCS-Tools for KNIME version 3.3.0.v201902130805 by Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

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

Input table

Output Ports

Table with normalized values

Table with statistics used for normalization

Best Friends (Incoming)

• Nominal Value Row Filter (17 %) ManipulatorStreamable
• Row Splitter (11 %) ManipulatorStreamable
• Group Loop Start (6 %) LoopStart
• Scorer (6 %) Other
• Concatenate (Optional in) (6 %) ManipulatorStreamable
• Nominal Value Row Splitter (6 %) ManipulatorStreamable
• Row Filter (6 %) ManipulatorStreamable
• GroupBy (6 %) Manipulator
• String Manipulation (6 %) ManipulatorStreamable
• Math Formula (6 %) ManipulatorStreamable
• Join Layout (3 %) Manipulator
• Normalize Plates (NPI) (3 %) Manipulator
• Normalize Plates (Z-Score) (3 %) Manipulator
• Plate Heatmap Viewer (3 %) Visualizer
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• Column Rename (3 %) ManipulatorStreamable
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• CSV Reader (< 1 %) Source
• Concatenate (< 1 %) ManipulatorStreamable
• Column Combiner (< 1 %) ManipulatorStreamable
• Column Rename (Regex) (< 1 %) ManipulatorStreamable
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Best Friends (Outgoing)

• GroupBy (19 %) Manipulator
• Plate Heatmap Viewer (12 %) Visualizer
• CSV Writer (12 %) SinkStreamable
• Concatenate (Optional in) (8 %) ManipulatorStreamable
• Normalize Plates (Z-Score) (4 %) Manipulator
• Outlier Removal (4 %) Source
• R Plot (4 %) Visualizer
• Loop End (4 %) LoopEnd
• Group Loop Start (4 %) LoopStart
• Column Combiner (4 %) ManipulatorStreamable
• Column Filter (4 %) ManipulatorStreamable
• Row Filter (4 %) ManipulatorStreamable
• Column Rename (4 %) ManipulatorStreamable
• RowID (4 %) ManipulatorStreamable
• Column Splitter (4 %) ManipulatorStreamable
• String Manipulation (4 %) ManipulatorStreamable
• Math Formula (4 %) ManipulatorStreamable
• Expand Well Position (< 1 %) Manipulator
• Range Filter (< 1 %) Manipulator
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• R Plot (< 1 %) 
• Table Writer (< 1 %) Sink
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• Cluster Assigner (< 1 %) PredictorStreamable
• PCA (< 1 %) Manipulator
• Row Splitter (< 1 %) ManipulatorStreamable
• Joiner (< 1 %) Manipulator
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Workflows

• 03_Normalization_of_screening_data

Installation

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