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:
- 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
- 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
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
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Best Friends (Outgoing)
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Workflows
Installation
To use this node in KNIME, install KNIME HCS Tools from the following update site:
Developers
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