[BioC] Help on experiment design

[Marcelo Brandão]

Thanks Mark.

Now, the data makes sense.
I draw the results on a heatmap (heatmap.2 from gplots), do you have
any idea on how to change the probes names to geneID? I am using
Nimblegen data and have an NDF file with all annotation.

Cheers and thanks again

Marcelo

Em 19 de agosto de 2010 01:29, Mark Cowley <m.cowley at garvan.org.au> escreveu:
> hi Marcelo,
>
> If you use that design matrix, then you'll need to also fit contrasts
>> designEsp <- cbind(controle=c(1,1,1,0,0,0),experimento=c(0,0,0,1,1,1))
>> fitEsp <- lmFit(exprs(summarized),designEsp)
> contr.matrix <- c(-1,1)
> fitEsp <- contrasts.fit(fitEsp, contr.matrix)
>> fitEsp <- eBayes(fitEsp)
>> topTable(fitEsp,coef=1, adjust = "fdr", n = 10)
>
> or use this design
>> designEsp2 <- cbind(intercept=c(1,1,1,1,1,1),expvscon=c(0,0,0,1,1,1))
>> fitEsp2 <- lmFit(exprs(summarized),designEsp2)
>> fitEsp2 <- eBayes(fitEsp2)
>> topTable(fitEsp2,coef=2, adjust = "fdr", n = 10)
>
> cheers,
> Mark
> On 19/08/2010, at 10:59 AM, Marcelo Brandão wrote:
>
>> Hello all!
>> I am analyzing a set with 6 microarrays, 3 controls and 3
>> experimentals. I am interested in look after differentially expressed
>> genes. My doubt, among a lot of else, is if my experiment is designed
>> correctly. I am currently using the following comands:
>>
>> designEsp <- cbind(controle=c(1,1,1,0,0,0),experimento=c(0,0,0,1,1,1))
>> fitEsp <- lmFit(exprs(summarized),designEsp)
>> fitEsp <- eBayes(fitEsp)
>> topTable(fitEsp,coef=2, adjust = "fdr", n = 10)
>>
>> is it the best way to infer different expression? I am using nimblegen
>> microarrays.
>>
>> Thanks in advance.
>>
>> Marcelo
>>
>> --
>> Marcelo Mendes Brandão
>> Postdoc fellow
>> Laboratório de Biologia Molecular de Plantas - ESALQ/USP
>> Website: http://bioinfo.esalq.usp.br
>> AtPIN: http://bioinfo.esalq.usp.br/atpin
>> SKYPE: mmbrand
>> Tel: (+55) 19 3429 4442
>>
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>
>



-- 
Marcelo Mendes Brandão
Postdoc fellow
Laboratório de Biologia Molecular de Plantas - ESALQ/USP
Website: http://bioinfo.esalq.usp.br
AtPIN: http://bioinfo.esalq.usp.br/atpin
SKYPE: mmbrand
Tel: (+55) 19 3429 4442