[BioC] getGene type not recognized

[James W. MacDonald]

Hi John,

You did find the problem. Ensembl has a very bad habit of changing the 
names they use for things, which makes maintaining biomaRt difficult for 
Steffen (and by extension, maintaining affycoretools for me).

<rant>
This is an example of what I would consider a gratuitous change - was it 
really necessary to change hgnc_symbol to hgnc? Did we gain something 
here? They did something similar with Mus musculus and Rattus norvegicus 
as well, changing it to markersymbol. Again, did we _really_ gain 
something by making these changes? Can't we just call it a symbol for 
all species and go on with our lives? >:#
</rant>

Whew, I feel better now ;-D

Best,

Jim



John Lande wrote:
> maybe I found the problems, but I will not be able to solve the issue:
> 
> if I run the getBM command, everything works but if in the attributes i put
> the field hgnc_symbol, it complains with the same error:
> 
> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol",
> "chromosome_name",  :
> Invalid attribute(s): hgnc_symbol
> Please use the function 'listAttributes' to get valid attribute names
> 
> if I run 'listAttributes' there is no hgnc_symbol, but hgnc. it is possible
> that by default getGene still have this parameter ad default.
> 
> 
> On 10/25/07, John Lande <john.lande77 at gmail.com> wrote:
>> Dear BioC,
>>
>>
>> I have the following problem with biomaRt packages:
>>
>> if I run any script with the function getGene, it seems it cannot
>> recognize the type field.
>>
>> it happen also with the example in the man of getGene:
>>
>>> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
>>> g = getGene( id = "1939_at", type = "affy_hg_u95av2", mart = mart)
>>> show(g)
>> Error in getBM(attributes = attrib, filters = type, values = id, mart =
>> mart) :
>> Invalid attribute(s): hgnc_symbol
>> Please use the function 'listAttributes' to get valid attribute names
>>
>> in general I am having problems with this packages in these day, when I am
>> using long input. I handled this using shorter input, and then merging the
>> results, but now I dont know what to do.
>>
>> by the way I am running ubuntu 7.04.
>>
>> did someone have the notice the same?
>>
>>
>>
>>> sessionInfo()
>> R version 2.6.0 (2007-10-03)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] Biobase_1.17.0        biomaRt_1.12.0        RCurl_0.8-3
>> [4] mouseLLMappings_2.0.1
>>
>> loaded via a namespace (and not attached):
>> [1] rcompgen_0.1-17 XML_1.93-2
>>
>>
>>
>> thank you
>>
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623