> Hello 
> 
> I have been using the GOstats package for analysis of my expession data and it has provided a great help to understand what is going on in my experiments. But I have a problem with one of the GO cathegories.
> 
> The output from GOstats using data from the U133A chip concerning the two cathegories GO:0000087 and GO:0007067
> GO.ID	Term	p.value	No.of.Genes	Total.number	
> GO:0000087	BP: M phase of mitotic cell cycle	3.14E-22	57	134	
> GO:0007067	BP: mitosis	8.61E-22	56	132	
> 
> But when I look into the probeset annotated to these two classes I get a very strange result for GO:0000087 
> Here follows the R code I have used:
> 
> library(GOstats)
> library(hgu133a)
> go.a <- as.list(hgu133aGO2PROBE)
> 
> GO.a.list <- unlist(go.a[["GO:0007067"]])
> length(GO.a.list)
> [1] 177
> 
> GO.a.list2 <- unlist(go.a[["GO:0000087"]])
> length(GO.a.list2)
> [1] 10
> 
> Why are these lists of so different lengths? When I look them up in AmiGO I get 730 for GO:0000087 and 715 for GO:0007067. The total number in my output represent the number of genes annotated to the GO cathegory in the A chip. I understand the results for GO:0007067; 177 is the number of probes and 132 the number of genes on the A chip.
> What is wrong with the annotation of the GO:0000087 cathegory, is there a fix to it, or have I just made a silly mistake?
> 
> Sincerly yours
> 
> Peder
> 
> PS I haven't recieved any list mails the last couple of days
> 
> ________________________________________________
> Peder Worning, PhD
> 
> Senior Scientist, Bioinformatics
> AstraZeneca R&D Lund
> S-221 87 Lund, Sweden
> 
> Tel:     +46 46 33 72 93
> Fax:    +46 46 33 71 64
> Email:  peder.worning@astrazeneca.com
> 
> 
> 

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