[BioC] Categories microarray data in functional profiles

[Marcelo Laia]

Hi,

I would like to do a category analysis on our data set.

I had learning vignettes on BioC Subview of Annotation and I found
goProfiles package very close what I think to do.

I have a set of cDNA in fasta format. This cDNA was analysed on one
color microarray.

I would like to group all these cDNA in relation to main function. For example:

100 macromolecular complex
25   ABC Transporter
36   Response to abiotic stress
(...)

After have selected the differentially expressed genes, I would like
to group they again and to compare with the previous total list. For
example, from the 100 genes in the group macromolecular complex I get
89 differentially expressed.

Could you tell me if there are some ways for to do this?

I think that I will need:

>From the FASTA get the GO categories
Group in main categories
Subset in accordance with differentially expressed genes
Make the comparison (plot graphs)

I would like to do something like the Figure 2, pag 5, from
http://dx.doi.org/10.1155/2007/17542

This is possible from FASTA?

Thank you very much

-- 
Marcelo Luiz de Laia
www.unesp.br
Jaboticabal - SP - Brazil
sip:marcelolaia at ekiga.net

"Você vê as coisas como elas são e pergunta: por quê? Mas eu sonho com
coisas que nunca foram e pergunto: por que não? " - Bernard Shaw