R package for the analysis of microtiter plate-based data. Data usually comes from spectrophotometers measuring optical density (OD), fluorescence or luminescence across time and includes blanks (e.g. medium only) and controls (e.g. bacterial strains without treatment).
Raw data is imported by device-specific import functions (e.g. import_tekanSpark), layout by a single import function (import_layout) based on a (very simple) template in excel format.
Raw data and layout are combined using a key created from plate and well (which are mandatory columns in both tables), for example the key P1_A1 from plate P1 and well A1. If multiple plates are combined, the run identifier can be added as part of the plate, for example run-10_P1 giving the key run-10_P1_A1. Wells included in raw data but not defined in the layout they will be automatically removed when data is combined. Wells that are defined in the layout must also be present in the data.
The PlateData object stores imported measurements ('raw') and 'layout' as data.frames. Internally, raw and layout are merged into 'combined' by the key and split into 'blank', 'control', and 'data'. Blank and control are summarized from replicates into mean and standard deviation (sd), the summarized values of data are stored in 'summary'. Control, data, and summary will be corrected by substracting the blank. Data and summary can be normalized by dividing by the corrected control. The measurement error (i.e. standard deviation of replicates) is propagated during data correction and normalisation.
Blank and controls are assigned by ...
The plate type (e.g. 6-well, 24-well, 96-well is determined automatically and stored as 'type').
There is no official release version yet, since the package is under development.
You can install the development version from GitHub using the remotes package:
remotes::install_github("OliverDietrich/PlateData@main")
Warning
Early development, no stable features.
Tutorials are available in vignettes that show typical use cases