[BioC] Designing a model with blocking and other interactions

Gordon K Smyth smyth at wehi.EDU.AU
Thu Apr 3 05:25:45 CEST 2014


Dear Eleanor,

   design1 <- model.matrix(~Family)
   design2 <- model.matrix(~mitoHap*Treatment)
   design <- cbind(design1,design2[,3:4])

Then test for the last coefficient.

Best wishes
Gordon

> Date: Tue, 1 Apr 2014 11:24:52 -0700
> From: Eleanor Su <eleanorjinsu at gmail.com>
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Designing a model with blocking and other interactions
>
> Hi All,
>
> I'm trying to set up a model matrix where I can look at the interaction
> between Treatment and mitochondrial haplotypes in my paired samples. These
> are the preliminary commands that I've set up:
>
>> rawdata<-read.delim("piRNAtotalcount<10.txt", check.names=FALSE,
> stringsAsFactors=FALSE)
>> y <- DGEList(counts=rawdata[,2:11], genes=rawdata[,1])
>> Family<-factor(c(6,6,9,9,11,11,26,26,28,28))
>> Treatment<-factor(c("C","H","C","H","C","H","C","H","C","H"))
>> mitoHap<-factor(c("S","S","S","S","S","S","D","D","D","D"))
>> data.frame(Sample=colnames(y),Family,Treatment,mitoHap)
>    Sample Family Treatment mitoHap
> 1   6C (S)      6         C       S
> 2   6H (S)      6         H       S
> 3   9C (S)      9         C       S
> 4   9H (S)      9         H       S
> 5  11C (S)     11         C       S
> 6  11H (S)     11         H       S
> 7  26C (D)     26         C       D
> 8  26H (D)     26         H       D
> 9  28C (D)     28         C       D
> 10 28H (D)     28         H       D
>
>> design<-model.matrix(?)
>
> I have 10 sequencing samples from 5 different families (a treatment and
> control sample from each family) and two different types of mitochondrial
> haplotypes. How do I set up a design where I can look at the interaction
> between the Treatments and mitoHap while still accounting for Family?
>
> Any help would be greatly appreciated. Thank you for your time.
>
> Best,
> Eleanor

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