Normalize Plates (POC)
HCS-Tools for KNIME version 3.3.0.v201902130805 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
Output Ports
Best Friends (Incoming)
GroupBy (9 %) 
Group Loop Start (7 %) 
Column Filter (7 %) Streamable
Nominal Value Row Filter (7 %) Streamable
Row Splitter (7 %) Streamable
Scorer (4 %) 
Concatenate (Optional in) (4 %) Streamable
Column Resorter (4 %) Streamable
Joiner (4 %) 
Column Rename (4 %) Streamable
String Manipulation (4 %) Streamable
Join Layout (2 %) 
Normalize Plates (NPI) (2 %) 
Vector Length Normalization (2 %) 
Normalize Plates (Z-Score) (2 %) 
Z-Primes (PC x NC) (2 %) 
Plate Heatmap Viewer (2 %) 
CSV Reader (2 %) 
File Reader (2 %) Streamable- Concatenate (2 %) Streamable
Column Combiner (2 %) Streamable
Number To String (2 %) 
Column Rename (Regex) (2 %) Streamable
Nominal Value Row Splitter (2 %) Streamable
Row Filter (2 %) Streamable
Renderer to Image (2 %) 
Rule Engine (2 %) Streamable
Math Formula (2 %) Streamable
XLS Reader(2 %) Deprecated- Show all 29 recommendations
Best Friends (Outgoing)
- GroupBy (13 %)
- Normalize Plates (Z-Score) (8 %)
- Plate Heatmap Viewer (6 %)
R Plot (4 %) 
CSV Writer (4 %) Streamable- Concatenate (Optional in) (4 %) Streamable
- Row Filter (4 %) Streamable
- Joiner (4 %)
- String Manipulation (4 %) Streamable
Expand Well Position (2 %) 
Range Filter (2 %) 
Outlier Removal (2 %) 
R Plot (2 %) 
R Snippet (2 %) 
Table Writer (2 %) 
Loop End (2 %) 
Variable Condition Loop End (2 %) - Group Loop Start (2 %)
Cluster Assigner (2 %) Streamable
PCA (2 %) - Column Combiner (2 %) Streamable
Constant Value Column (2 %) Streamable- Column Filter (2 %) Streamable
- Row Splitter (2 %) Streamable
- Column Rename (2 %) Streamable
RowID (2 %) Streamable
Column Splitter (2 %) Streamable- Rule Engine (2 %) Streamable
Conditional Box Plot (2 %) - Bar Chart (JavaScript) (2 %)
- Math Formula (2 %) Streamable
Math Formula (Multi Column) (2 %) Streamable- Show all 32 recommendations
Workflows
Installation
To use this node in KNIME, install HCS-Tools for KNIME from the following update site: