[BioC] the design matrix again

Gordon K Smyth smyth at wehi.EDU.AU
Fri Jul 23 01:13:56 CEST 2010


Looks correct.

Gordon


> Date: Tue, 20 Jul 2010 17:44:07 -0400
> From: HuW at mskcc.org
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] the design matrix again
>
>
> Hi everyone,
>
> I know my question is answered in some extent on mail list. But I am 
> still not feel very confidence about my design. I really appreciate if 
> anyone can help me on this.
>
> the data set is about the patients before and after treatment. for 
> example, for 3 patients. I want to find out the genes that changed 
> expression before and after treatment. if I have 3 patients, I did like 
> this:
>
>> design
>  patient1 patient2 patient3 treatment14
> 1        1        0        0           0
> 2        0        1        0           0
> 3        0        0        1           0
> 4        1        0        0           1
> 5        0        1        0           1
> 6        0        0        1           1
> attr(,"assign")
> [1] 1 1 1 2
> attr(,"contrasts")
> attr(,"contrasts")$patient
> [1] "contr.treatment"
>
> attr(,"contrasts")$treatment
> [1] "contr.treatment"
>
>> eset.rma.fit = lmFit(eset.rma, design);
>> eset.rma.bayes = eBayes(eset.rma.fit);
>> topTable(eset4.rma.bayes, coef = "treatment14", adjust = "BH");
>
> thank you very much.
>
> Wenhuo Hu

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