immunoassay-package: Functions to aid fitting and batch processing of immunoassay...

Description Details Author(s) See Also


The package immunoassay contains several functions to aid batch processing of data from immunoassay runs, although currently only the loading of Multiplex data is implemented. There are functions to load data: read.multiplex, fit a choice of sigmoidal models: sigfit, and a batch-processing function to process a whole directory of data files, validate the results and produce reports: batch. There also are associated print, summary and plot methods, that can be used in report templates. Function batch can produce text or LaTeX reports, where the latter are made based upon project-specific templates, that are separate R/Sweave scripts. These functions are in early stage of development - they've been tested on data from a single instrument platform, in a single study environment, and with 2- and 3-analyte runs only. In other projects that utilize different plate layout, or with greater number of analytes, or simply with different sample-naming conventions, these functions may require major modifications in order to work properly. Nevertheless, this package proved remarkably useful in our laboratory allowing for fast processing of large amounts of data (projects of 70 and more runs) and creation of nice reports and summary plots.


Package: immunoassay
Type: Package
Version: 0.41
Date: 2011-05-02
License: GPL-2
LazyLoad: yes

There are three main functions in this package:


A function to extract data from a multiplex .csv file.


A function that fits a choice of sigmoidal models to the data.


A batch-processing function that uses the above two functions
to process folders of data files.

The functions in the immunoassay package define two classes: ima class for raw immunoassay data, and sigfit class for fitted sigmoidal models. For these classess print, summary and plot methods exist. See help on individual functions for more details.

Additionally the immunoassay package relies on several global vectors:


A data frame containing kit information (concentrations of Standards and QCs for every analyte) for the kits used in producing the data to be processed. This is a required element - functions will not run without it, however the batch function will load the kit data automatically if it exists in proper location and has a proper name. For more information, see help on read.kits and batch functions.


A list created by batch function, that contains equation coefficients for every fitted model. This list is used by the fitting function to calculate starting values for subsequent fits. This element is not required to start (default starting values will be used), but it will be automatically created. For more information, see help on batch function.


A list of all the model settings for the data files in the project folder - used by the batch function. It is not required to start, but will be automatically created by this function. If the processing fails, the records in this list can be modified and re-used. For more information, see help on batch function.


A pointer to the environment of the batch function, for use within the Sweave project report templates. It is automatically created by the batch function. It's necesary due to known shortcoming of Sweave that can work in the global environment only.


Michal J. Figurski, PhD and Leslie M. Shaw of the Biomarker Research Laboratory, University of Pennsylvania, Philadelphia, PA.

See Also

batch, read.multiplex, read.kits and sigfit.

immunoassay documentation built on May 2, 2019, 4:45 p.m.