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
- 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
Best Friends (Incoming)
- Row Filter (8 %) Streamable
- Example Data (6 %)
- Group Loop Start (6 %)
- Column Rename (6 %) Streamable
- Filter Apply (5 %) Streamable
- Show all 53 recommendations
Best Friends (Outgoing)
- Image To Table (18 %)
- Loop End (13 %)
Excel Writer (XLS)(10 %) Deprecated- Image Writer (Port) (8 %)
- CSV Writer (7 %) Streamable
- Show all 23 recommendations
Workflows
05_Dose_Response (KNIME Hub)
Installation
To use this node in KNIME, install KNIME HCS Tools from the following update site:
A zipped version of the software site can be downloaded here.
You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.
Developers
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.