Hi,I am new to gene ontology analysis and i need help for the following question: i used fold change to find my different genes in Microsoft excel, then i get the annotation for the different genes, here comes the problem, the next step i should would be do gene ontology analysis,right?and if i would like to find genes which involve in special function, such as "lipid", how can i do that? Detail with example will be appreciated.
I think you might want to try to fix your general analysis and do some reading to familiarise yourself with the background and technology. If you want to use Bioconductor, which I would advise, have a look at the Bioconductor page. There is a lot of documentation available there as well as on many other places on the web. This one, by Thomas Girke, UC Riverside, is also very helpful. It includes, among others, sections about the 'Analysis of Differentially Expressed Genes' and 'Gene Ontologies'.
Regarding your analysis pipeline, have a look at the Using Bioconductor for Microarray Analysis page and references therein as a starting point. The book Bioconductor Case Studies will provide all you need to know and much more.
Hope this helps.
What you are trying to do is called an over-enrichment analysis, over-representation analysis or a functional enrichment test. There are a lot of web-based tools for doing this.