[BioC] Categories microarray data in functional profiles

Marcelo Laia marcelolaia at gmail.com
Sat Jul 19 20:53:10 CEST 2008


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

This is possible from FASTA?

Thank you very much

Marcelo Luiz de Laia
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

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