[BioC] question about model.matrix and makeContrasts for limma

[Ou, Jianhong]

Hi James,

Thanks a lot. I got it.

Yours sincerely,

Jianhong Ou

LRB 710
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605




On 4/10/13 9:47 AM, "James W. MacDonald" <jmacdon at uw.edu> wrote:

>Hi Jainhong Ou,
>
>On 4/10/2013 9:24 AM, Ou, Jianhong wrote:
>> Hi All,
>>
>> I have samples like this:
>> Targets.txt>>
>> Filename group replicates
>> V1            vec     rep1
>> V2            vec     rep2
>> V3            vec     rep3
>> A1            aec     rep1
>> A2            aec     rep2
>> A2            aec     rep2
>> C1             cec     rep1
>> C2             cec     rep2
>> C3             cec     rep3
>> D1             dec     rep1
>> D2             dec     rep2
>> D3             dec     rep3
>> E1             eec     rep1
>> E2             eec     rep2
>> E3             eec     rep3
>>
>> If I want to compare group vec to all the others, is this correct I
>>create model matrix and make contrasts like this,
>> design<- model.matrix(~-1+group)
>> colnames(design)<- gsub("^group","",colnames(design))
>> contrast.matrix<- makeContrasts(contrasts="vec-(aec+cec+dec+eec)/4",
>>levels=design)
>
>That would be the conventional way of doing it.
>
>>
>> Or should I do it like,
>> block<- factor(c(rep("b1", 3), rep("b2",12)))
>> design<- model.matrix(~-1+block+block:group)
>> colnames(design)<- gsub("^block","",colnames(design))
>> contrast.matrix<- makeContrasts(contrasts="b1-b2", levels=design)
>
>That would not be a way to do it. Did you look at the design matrix you
>created? If so did you notice that you have four columns that contain
>only zeros? What did you hope to accomplish with the block:group
>specification?
>
>You can always check for problems with the nonEstimable() function in
>limma:
>
> > nonEstimable(model.matrix(~0+block+block:group))
>[1] "block1:group2" "block1:group3" "block1:group4" "block1:group5"
>[5] "block2:group5"
>
>Best,
>
>Jim
>
>
>>
>> Thanks in advance for you help.
>>
>> Yours sincerely,
>>
>> Jianhong Ou
>>
>> LRB 710
>> Program in Gene Function and Expression
>> 364 Plantation Street Worcester,
>> MA 01605
>>
>> 	[[alternative HTML version deleted]]
>>
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>
>-- 
>James W. MacDonald, M.S.
>Biostatistician
>University of Washington
>Environmental and Occupational Health Sciences
>4225 Roosevelt Way NE, # 100
>Seattle WA 98105-6099
>