[BioC] KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism

[zhao shilin]

Dear Stefano,

I've tested species Pseudovibrio FO-BEG1 ("psf" in KEGG database) and found
it was imported into KEGG database in 2013 (
http://www.genome.jp/kegg-bin/show_organism?org=psf). But KEGG.db package
was updated until 2012. I think that is the reason for the error message.
Now I provide a new parameter "download_latest" in "find_enriched_pathway"
function of KEGGprofile package, you can find it in KEGGprofile version
1.7.6 on Bioconductor. But I think it is still in the develop channel
of Bioconductor so you may not able to see it immediately. You can download
it from my github (https://github.com/slzhao/KEGGprofile) now.

Here is the test codes:
library("KEGGprofile")
species<-"psf"
download_KEGGfile(pathway_id="00010",species=species)
result<-parse_XMLfile(pathway_id="00010",species=species)
genes<-unique(result[9:40,1])
genes
enriched<-find_enriched_pathway(gene=genes,species=species,
download_latest=TRUE)
enriched$stastic

Please let me know if you have any other questions.

Best,
Shilin



2014-09-14 2:07 GMT-05:00 stefano romano <stfn.romano at gmail.com>:

> Dear Shilin,
> thank you very much for your answer.
> The organism I am using is Pseudovibrio FO-BEG1.
>
> I got the same problme with both GI and locus_tag.
>
>
> These are some GI:
> 359341142
> 359341144
> 359341148
> 359341161
> 359341162
> 359341167
> 359341173
> 359341177
> 359341200
> 359341208
> 359341211
>
> And these are some locus-tag:
>
> PSE_3630PSE_4282PSEp_0373PSE_1587PSE_1679PSE_1691PSE_1086PSE_0648PSE_1681
> PSE_2573
>
> Thanks again for your help.
>
> Best,
>
> Stefano
>
> 2014-09-14 3:36 GMT+02:00 zhao shilin <zhaoshilin at gmail.com>:
>
>> Dear Stafano,
>>
>> I think the ID from the non model organism may cause the error. Would
>> you please tell me the specie you tested and send me some of your genes.
>> So that I can have a try.
>> Thank you!
>>
>> Best,
>> Shilin
>>
>> 2014-09-13 3:03 GMT-05:00 stefano romano <stfn.romano at gmail.com>:
>>
>>> Hi,
>>>
>>> I am using KEGGprofile to perform KEGG enrichment for a non model
>>> organism.
>>> Using the data from the R documentation i perfectely obtaine the
>>> enrichment.
>>>
>>> >data(pho_sites_count)
>>> >genes<-names(rev(sort(pho_sites_count[,1]))[1:300])
>>> > summary(genes)
>>>    Length     Class      Mode
>>>       300 character character
>>> > is.vector(genes)
>>> [1] TRUE
>>> >pho_KEGGresult<-find_enriched_pathway(genes,specis='hsa')
>>>
>>> However, when I use my datasets, which I submit as character vector with
>>> NCBI ID, I get the following error:
>>>
>>> Error in phyper(kegg_result_length[x], keggpathway2gene_length[x],
>>> length(unique(unlist(keggpathway2gene))) -  :
>>>   Non-numeric argument to mathematical function
>>>
>>> Any suggestion how to overcome this problem?
>>>
>>> Thank you very much.
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>
>

	[[alternative HTML version deleted]]