Dear Thomas,

Thank you! It worked!
Have a nice weekend!

Priscila

On Sat, May 9, 2009 at 11:03 AM, Thomas Hampton <
Thomas.H.Hampton@dartmouth.edu> wrote:

> It isn't too hard to make your own volcano, and I do it
> all the time. You may find it easier to just use the R
> plot command like this rather than trying to wangle something in
> your bioconductor package:
>
> plot(M, -log10(P), pch = '.')
>
>
> assuming M is your vector of log2 fold differences and P
> is a vector of whatever you prefer as a significance measure.
>
> A very nice thing about doing it yourself is that you can then
> highlight a set of genes that interest you:
>
>
> points(M[interesting], -log10(P[interesting]), col = "red", pch = 16)
>
>
> Of course you can add all sorts of labels in the plot command.
>
> Tom
>
>
>
>
> On May 9, 2009, at 9:47 AM, Priscila Grynberg wrote:
>
>  Dear BioCs,
>> I'd like to make a volcano plot, but instead of B value, I want to plot
>> the
>> adjusted p-values. Can I do that? Fold-changes X adjusted p-values?
>>
>> I have oligo slides. Do you need any further information for that?
>>
>> Thanks,
>>
>> Priscila
>>
>> --
>> Priscila Grynberg, B.Sc., M.Sc.
>> Doutoranda em Bioinformática (Bioinformatics D.Sc student)
>> Laboratório de Genética Bioquímica
>> Universidade Federal de Minas Gerais
>> Tel: +55 31 3409-2628
>> CV: http://lattes.cnpq.br/8808643075395963
>>
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>>
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>>
>
>


-- 
Priscila Grynberg, B.Sc., M.Sc.
Doutoranda em Bioinformática (Bioinformatics D.Sc student)
Laboratório de Genética Bioquímica
Universidade Federal de Minas Gerais
Tel: +55 31 3409-2628
CV: http://lattes.cnpq.br/8808643075395963

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