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@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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