[BioC] the design matrix again
HuW at mskcc.org
HuW at mskcc.org
Tue Jul 20 23:44:07 CEST 2010
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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