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