[BioC] topGO question

Sun Sep 14 10:02:09 CEST 2008

Hi Adrian,

thanks for your reply.

I passed the annFUN.gene2GO  and got  no errors.  allGo contains no NA 
and no NULL.
go_list is a list of character vectors:

 > str(go_list2)
List of 9
 $ TM00000001: chr [1:2] "GO:0009058" "GO:0016757"
 $ TM00000002: chr [1:38] "GO:0003700" "GO:0007275" "GO:0005634" 
"GO:0009414" ...
 $ TM00000003: chr [1:38] "GO:0003700" "GO:0007275" "GO:0045449" 
"GO:0005634" ...
 $ TM00000004: chr [1:5] "GO:0005634" "GO:0045449" "GO:0009943" 
"GO:0009947" ...
 $ TM00000005: chr [1:13] "GO:0016165" "GO:0040007" "GO:0006952" 
"GO:0009695" ...
 $ TM00000006: chr [1:38] "GO:0003700" "GO:0007275" "GO:0045449" 
"GO:0005634" ...
 $ TM00000007: chr [1:38] "GO:0003700" "GO:0007275" "GO:0045449" 
"GO:0005634" ...
 $ TM00000009: chr [1:42] "GO:0016301" "GO:0004672" "GO:0004674" 
"GO:0009733" ...
 $ TM00000010: chr [1:8] "GO:0009736" "GO:0005886" "GO:0004673" 
"GO:0009884" ...

And, here is my sessionInfo:

 > sessionInfo()
R version 2.7.2 (2008-08-25)
i486-pc-linux-gnu

locale:
LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=de_DE.UTF-8;LC_ADDRESS=de_DE.UTF-8;LC_TELEPHONE=de_DE.UTF-8;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=de_DE.UTF-8

attached base packages:
 [1] splines   grid      tcltk     tools     stats     graphics  grDevices
 [8] utils     datasets  methods   base    

other attached packages:
 [1] maizeprobe_2.2.0     matchprobes_1.12.1   maizecdf_2.2.0     
 [4] GO_2.2.0             topGO_1.8.1          SparseM_0.78       
 [7] biomaRt_1.14.1       RCurl_0.9-4          GOstats_2.6.0      
[10] Category_2.6.0       genefilter_1.20.0    survival_2.34-1    
[13] RBGL_1.16.0          annotate_1.18.0      xtable_1.5-3       
[16] GO.db_2.2.0          AnnotationDbi_1.2.2  RSQLite_0.7-0      
[19] DBI_0.2-4            graph_1.18.1         qvalue_1.14.0      
[22] maanova_1.10.0       arrayQuality_1.18.0  RColorBrewer_1.0-2 
[25] gridBase_0.4-3       hexbin_1.14.0        colorspace_0.95    
[28] convert_1.16.0       marray_1.18.0        tkWidgets_1.18.0   
[31] DynDoc_1.18.0        widgetTools_1.16.0   statmod_1.3.6      
[34] vsn_3.6.0            lattice_0.17-14      affy_1.18.2        
[37] preprocessCore_1.2.1 affyio_1.8.1         Biobase_2.0.1      
[40] limma_2.14.6         rkward_0.4.9       

loaded via a namespace (and not attached):
[1] cluster_1.11.11 XML_1.96-0    

Would be very glad if you have any idea, what went wrong. Thanks,
Heike

Adrian Alexa schrieb:
> Hi Heike,
>
> it seems that there is a problem with the go_list object. It should be
> a list of character vectors. However, it is hard to tell what is wrong
> with just the information you provided. Please also post the session
> info such that we know which version of the software are you using.
>
> The error is with the annFUN.gene2GO() function. if the go_list is
> correct, than the following line should pass without error:
>
> go2genes <- annFUN.gene2GO(whichOnto = "MF", gene2GO = go_list)
>
> If you get an error here, can you post the results of the following lines:
>
> allGO = unlist(go_list, use.names = FALSE)
> str(allGO)
> sum(is.na(allGO))
> sum(is.null(allGO))
>
>
> Regards,
> Adrian
>
>
>
>
>
>
> On Fri, Sep 12, 2008 at 11:42 AM, Heike Pospisil
> <pospisil at zbh.uni-hamburg.de> wrote:
>   
>> Hello list,
>>
>> I am trying to use topGO for GO enrichment analysis. I have data from an
>> array which is still not supported by BioC (maize array).
>>
>> I have a mapping of genes to GO terms named go_list:
>>
>> $TM00000001
>> [1] "GO:0009058" "GO:0016757"
>>
>> $TM00000002
>> [1] "GO:0003700" "GO:0007275" "GO:0005634" "GO:0009414" "GO:0016563"
>> [6] "GO:0009737" "GO:0045449" "GO:0010072" "GO:0046982" "GO:0009651"
>> [11] "GO:0009733" "GO:0009723" "GO:0009734" "GO:0048527" "GO:0042803"
>> [16] "GO:0009867" "GO:0010150" "GO:0009825" "GO:0009908" "GO:0003713"
>> [21] "GO:0051607" "GO:0009790" "GO:0010014" "GO:0048467" "GO:0030528"
>> [26] "GO:0009741" "GO:0009735" "GO:0010089" "GO:0009834" "GO:0009901"
>> [31] "GO:0009611" "GO:0008361" "GO:0009416" "GO:0009620" "GO:0009744"
>> [36] "GO:0009753" "GO:0009751" "GO:0010199"
>>
>> Moreover, the geneList is the named factor that indicates which genes are
>> interested:
>>     
>>> str(geneList)
>>>       
>> Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
>> - attr(*, "names")= chr [1:56321] "MZ00000001" "MZ00000002" "MZ00000003"
>> "MZ00000004" ...
>>
>> I have used annFUN.gene2GO  as an annotation function:
>>
>> GOdata<-new("topGOdata",ontology="MF",allGenes=geneList,annot=annFUN.gene2GO,gene2GO=go_list)
>>
>> Unfortunately,  I got the following error message:
>> Building most specific GOs .....Error in order(allGO) : argument 1 is not a
>> vector
>>
>> Does anybody have an idea what is wrong in my code?
>>
>> Thanks and best,
>> Heike
>>
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>>     
>
>