07.SingleChannel {limma} | R Documentation

## Topic: Individual Channel Analysis of Two-Color Microarrays

### Description

This page gives an overview of the LIMMA functions fit linear models to two-color microarray data in terms of the log-intensities rather than log-ratios.

The function `intraspotCorrelation` estimates the intra-spot correlation between the two channels. The regression function `lmscFit` takes the correlation as an argument and fits linear models to the two-color data in terms of the individual log-intensities. The output of `lmscFit` is an `MArrayLM` object just the same as from `lmFit`, so inference proceeds in the same way as for log-ratios once the linear model is fitted. See 06.LinearModels.

The function `targetsA2C` converts two-color format target data frames to single channel format, i.e, converts from array-per-line to channel-per-line, to facilitate the formulation of the design matrix.

### Author(s)

Gordon Smyth

### See Also

01.Introduction, 02.Classes, 03.ReadingData, 04.Background, 05.Normalization, 06.LinearModels, 07.SingleChannel, 08.Tests, 09.Diagnostics, 10.GeneSetTests, 11.RNAseq

[Package limma version 3.42.2 Index]