[BioC] Help on experiment design

[Mark Cowley]

Hi Marcelo,
take a look at the annotation packages here: http://bioconductor.org/packages/release/AnnotationData.html

you'll need to do the mapping from probe to gene before running heatmap.2, since heatmap.2 won't do that conversion for you

cheers,
Mark

On 20/08/2010, at 12:09 AM, Marcelo Brandão wrote:

> 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
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
>> 
> 
> 
> 
> -- 
> 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