[BioC] LIMMA makeContrasts question

T S tsm8015 at gmail.com
Fri Dec 1 03:23:15 CET 2006


I am a complete beginner to Linear Models and using the LIMMA package.
First I have a general question as to what are good intro texts
explaining Linear Models in general.

I also have the following specific question. I have 4 samples: wild
type (WT), a sample were I turn on a pathway (ON) and two where I
knock down the same pathway in two different ways (KO1, KO2). I want
to find genes that are significantly changed with the following

   sign(log(ON/WT)) == -sign(log(KO1/WT)) and -sign(log(KO2/WT))

would the following design and contrast matrix be correct

type = is a factor with levels WT, ON, KO1, KO2
design = model.matrix(~0 + type)
cm = makeContrasts(eff = (ON - WT) - (KO1 - WT) - (KO2 - WT), levels=design)

Any help or guidence would be greatly appreciated. Also pointers to
suitable documentation explain such matters would be great.

Thanks in advance

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