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Dose Response (R)

HCS-Tools for KNIME version 4.0.0.v202007151505 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:

LL.3 : Three-parameter logistic
LL.4 : Four-parameter logistic (default)
LL.5 : Five-parameter logistic
W1.2 : Two-parameter Weibull
W1.3 : Three-parameter Weibull
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:

Data points - single measurements
SEM - standard error of the mean (default)
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)

Row Filter (8 %) Streamable
Example Data (6 %)
Group Loop Start (6 %)
Column Rename (6 %) Streamable
Filter Apply (5 %) Streamable
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Best Friends (Outgoing)

Image To Table (18 %)
Loop End (13 %)
~~Excel Writer (XLS)~~ (10 %) Deprecated
Image Writer (Port) (8 %)
CSV Writer (7 %) Streamable
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Workflows

05_Dose_Response (KNIME Hub)

Installation

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

KNIME 4.2

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