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

[Marcus Davy]

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.

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch 
https://stat.ethz.ch/mailman/listinfo/bioconductor

______________________________________________________

The contents of this e-mail are privileged and/or confidenti...{{dropped}}