Description Author(s) See Also

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.

Gordon Smyth

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

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