vsn - Variance stabilization and calibration for microarray data

The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

Last updated 5 months ago

microarrayonechanneltwochannelpreprocessing

8.33 score 51 dependents 924 scripts 7.6k downloads

splots - Visualization of high-throughput assays in microtitre plate or slide format

This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package.

Last updated 5 months ago

visualizationsequencingmicrotitreplateassay

3.30 score 454 downloads