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Dose Response (R)

HCS-Tools for KNIME version 4.0.0.v201906200802 by Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

Calculates and visualizes dose response curves. This is achieved by fitting several non-linear regression models to your data.
Measurements are grouped per Compound and Concentration (see Options).
Measurements from a zero concentration are used to calculate the fit but are not displayed in the plot because of its logarithmic scale.
For a conceptual and technical overview have a look at "Bioassay Analysis using R", Ritz and Streibig, 2005, 5:12, Journal of Statistical Software.

IMPORTANT:
This node is using R as back end, make sure that Rserve is running somewhere, and KNIME is accordingly configured (KNIME->Preferences). HCS-Tools Wiki

Options

Script Editor

Parameters of interest
The assay parameters for which a dose response analysis should be carried out.
Compound
The column containing the compound information (group1)
Concentration
The column containing the concentrations (group2)
Plot title
Adds a custom main title to the plot
Regression Model
The following models (referred to their abbreviation in the configuration dialog) are supported:
  1. LL.3 : Three-parameter logistic
  2. LL.4 : Four-parameter logistic (default)
  3. LL.5 : Five-parameter logistic
  4. W1.2 : Two-parameter Weibull
  5. W1.3 : Three-parameter Weibull
  6. W1.4 : Four-parameter Weibull
For a mathematical model definition see Package 'drc'
Plotting Options
Several plot options additional to the dose response curve are available:
  1. Data points - single measurements
  2. SEM - standard error of the mean (default)
  3. SD - standard deviation
Parameter constraints
Allows to set constraints for some or all parameters of the model. This requires knowledge about the model structure, which can be obtained easily using R (e.g. just type ?LL.4 for the configuration of the 4-parametric logistic model. Use NA for no constraint.
Example for LL.4 which imposes a upper limit at 3: NA, NA, 3, NA

Chunk Settings

Several settings
Settings to transfer the data between KNIME and R in chunks (only necessary for very big tables) For documentation please check out the node description of the RSnippet node.

Output Options

Several settings
Settings to control plot size and whether it should be exported as file. For documentation please check out the node description of the RPlot node.

Input Ports

A table with dose response data

Output Ports

A table which contains ic50s, model parameters, and error estimates
The generated dose response curve plotted as PNG-image
An R list with all dose response models for further analysis

Views

R-Plot
R-Plot with dose response curve

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.0
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