[BioC] Help on experiment design

[Marc Carlson]

Hi Marcelo,

It sounds like you might want to make a custom annotation package.  Is
that the case?  If so, you should read the SQLForge vignette in the
AnnotationDbi package.

You can find that here:
http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html

Does that answer your question?


  Marc



On 08/23/2010 12:58 PM, Marcelo Brandão wrote:
> Hi there
> I am completely lost on how to map from probe to gene using nimblegen
> data. Where can I find a tutorial or some kind of help. I see that I
> need to generate a package, but I need my tabular file in a specific
> order, does anyone knows what this order may be?
>
> Cheers
>
> Marcelo
>
>
> Em 20 de agosto de 2010 00:50, Mark Cowley <m.cowley at garvan.org.au> escreveu:
>   
>> 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
>>>       
>>
>>     
>
>
>