[BioC] Designing a model with blocking and other interactions

[Eleanor]

Hi Gordon, 

Could you elaborate on how to test for the last coefficient? Sorry if that's an elementary question. I'm a master's student working with VERY limited resources in my department, and I appreciate all the help I can get. Thanks for all your help! 

Best, 
Eleanor 

On Apr 2, 2014, at 8:25 PM, Gordon K Smyth <smyth at wehi.EDU.AU> wrote:

> 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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