[BioC] [limma] How do I do to obtain DE genes in Time CourseExperiments?

[Marcelo Luiz de Laia]

Hi,

I look at the slot genes in fit2 (fit2$genes) and selected.dif. Both 
have the some number of genes.

But, when I try

fit2$genes[selected.dif,]

I get a error message:

Error in "[.default"(fit2$genes, , selected.dif) : 
        incorrect number of dimensions

If I use topTable and set the coef slot to 1, 2 or 3 I get the DE genes, but, I suppose that in these case the list of genes are different from the example in usersguide. Or not?

I make 3 contrast before fit the values, then I get 3 coef in fit2. Could be this the cause of error message? In the usersguide there are 2 contrasts.

Thanks

Marcelo



Marcus Davy escreveu:

>The gene annotation information is usually a list component called 'genes' within the output object from lmFit, and eBayes. This gets used in the construction of the table of the top-ranked genes using topTable.
>
>Have a look at fit2$genes (for your object fit2).
>
>Your R expression has just provided a logical vector of corrected p-values for genes <0.05 based on the B&H's stepup FDR control, try:
>
>fit2$genes[selected.dif,]
>
>
>Marcus
>
>  
>
>>>>Marcelo Luiz de Laia <mlaia at fcav.unesp.br> 17/02/2005 12:08:53 PM >>>
>>>>        
>>>>
>Hi,
>
>I have been analyse a time course experiment with limma and I get the 
>end of section 16 in userguide very well.
>
>But, I don't know how do I do to get the names of genes differentially 
>expressed!
>
>For example, I do:
>
>selected.dif <- p.adjust(fit2$F.p.value, method="fdr") < 0.05
>
>In object *selected.dif* I see that there are a lot of TRUE, but I don't 
>know is their names!
>
>Any help is very appreciated.
>
>Marcelo
>
>
>  
>


-- 
No virus found in this outgoing message.
Checked by AVG Anti-Virus.