[BioC] Problem with biomaRt and retrieving annotation for the chip "affy_huex_1_0_st_v2"

[James MacDonald]

Hi Nenad,

Please don't take things off list. The list archives are intended to be a resource of questions and answers for others to use.

I am not sure why you are doing the query that you show. Do you _really_ want to get everything on that chip? That is a huge amount of data, which is not ideal for an interactive web-based query system. In general the idea is to use biomaRt to get annotations for some set of probesets that are interesting for some reason. So for instance, this works:

> tst <- getBM("affy_huex_1_0_st_v2", "ensembl_gene_id", "ENSG00000146556", mart)
> tst
   affy_huex_1_0_st_v2
1              3612188
2              2390573
3              2501592
4              3674797
5              3195860
6              2501576
7              3612191
8              3612192
9              3195888
10             2501594
11             3612187
12             2501583
<snip>

Best,

Jim



James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
>>> Nenad Bartonicek <nbartonicek at gmail.com> 03/11/09 9:09 AM >>>
Hi Jim,

Thank you for a quick reply. I did try with
 >data=getBM(attributes="affy_huex_1_0_st_v2",value=T, mart=ensembl)
Error in postForm(paste(martHost(mart), "?", sep = ""), query =  
xmlQuery) :
   transfer closed with outstanding read data remaining

and it is the same thing.

When I use other arrays it is ok. For example:
 >data=getBM(attributes="affy_hugene_1_0_st_v1", mart=ensembl)
 > head(data)
   affy_hugene_1_0_st_v1
1               8165646
2               8165644
3               8174970
4               7946565
5               7946563
6               8089038

Thanks,

Nenad
On 11 Mar 2009, at 13:03, James W. MacDonald wrote:

> Hi Nenad,
>
>
>
> Nenad Bartonicek wrote:
>> Hello,
>> There seems to be a problem in retrieving annotation from the chip   
>> "affy_huex_1_0_st_v2".
>> >library(biomaRt)
>> >ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl")
>> Checking attributes and filters ... ok
>> #check if "affy_huex_1_0_st_v2" is a valid attribute
>> >attributes=listAttributes(ensembl)
>> >grep("affy_huex_1_0_st_v2",attributes[,1])
>> [1] 13
>> #collect data
>> >data=getBM(attributes="affy_huex_1_0_st_v2", mart=ensembl)
>
> You are not asking for any data here. Do you get the same result if  
> you include some values for the filter and values arguments?
>
> Best,
>
> Jim
>
>
>> Error in postForm(paste(martHost(mart), "?", sep = ""), query =   
>> xmlQuery) :
>>   transfer closed with outstanding read data remaining
>> > sessionInfo()
>> R version 2.8.1 (2008-12-22)
>> i386-apple-darwin8.11.1
>> locale:
>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>> attached base packages:
>> [1] stats     graphics  grDevices datasets  tools     utils      
>> methods
>> [8] base
>> other attached packages:
>> [1] biomaRt_1.16.0    R.utils_1.1.1     R.oo_1.4.6          
>> R.methodsS3_1.0.3
>> [5] Biobase_2.2.2
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.94-1 XML_2.3-0
>> Thank you for your help,
>> Nenad
>> Nenad Bartonicek
>> European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge
>> CB10 1SD
>> United Kingdom
>> tel: +44-755-435-9057
>> 	[[alternative HTML version deleted]]
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>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826


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