How do I relate the gene list by annotation files to the actual gene ontology website?

[Karen]

I know how to make "Gene list by annotation files" by selecting "Gene
ontology" from the "annotation category" and then "exporting
expression file" to get all expression data for these probes out of my
dataset. I find this very useful. However, I want to know how to
link the gene ontology annotation files to a particular gene ontology
number.
E.g. for extracellular matrix the annotation file has 299 in brackets,
when I look on the gene ontology website it says that there are 611
genes in the extraceullar matrix category and the GO number is GO:
0031012. Is this the same list? When I look at the actual genes in
each list (the dchip annotation file and GO term 0031012 list) they
appear to be different. I would like to be able to find the exact GO
number so I can write it up my paper.

Can anyone help?

In addition does anyone know why when you export expression file data
and calculate the fold change in excel it is different from the way
dchip does it...probably a stupid question!!!

Many thanks,

Karen

[Cheng Li]

Karen,

The GO IDs are in the file in the same directory as gene info file and named
as "**** gene_info Gene Onotology.xls".

The group mean issue is explained here:
http://biosun1.harvard.edu/complab/dchip/compare%20sample.htm#group_mean

Cheng