[Bioc-devel] FW: I have a problem with GO:0000087 "M phase ofmitotic cell cycle"
Goeman, J.J. (MSTAT)
J.J.Goeman at lumc.nl
Tue Nov 21 11:00:03 CET 2006
Try using as.list(hgu133aGO2ALLPROBES). This gives all genes annotated
to a GO term, while as.list(hgu133aGO2PROBE) gives the genes annotated
to the term but not to its children.
By the way: I think this question would have been better put to the
ordinary bioconductor at stat.math.ethz.ch mailing list.
> -----Original Message-----
> From: bioc-devel-bounces at stat.math.ethz.ch
> [mailto:bioc-devel-bounces at stat.math.ethz.ch] On Behalf Of
> Worning, Peder
> Sent: 21 November 2006 10:45
> To: bioc-devel at stat.math.ethz.ch
> Subject: [Bioc-devel] FW: I have a problem with GO:0000087 "M
> phase ofmitotic cell cycle"
> > 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)
> >  177
> > GO.a.list2 <- unlist(go.a[["GO:0000087"]])
> > length(GO.a.list2)
> >  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 at astrazeneca.com
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