Hi Khademul,

I just tried to run your code and it worked fine. It might be due to server
overload at the moment you submitted your query which lead to query time
out. Could you please try again to see if it works for you? Thanks!

> mart=useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",
host="may2009.archive.ensembl.org <http://may2009.archive.ensembl.org/> ",
path="/biomart/martservice",archive=FALSE)
> Checking attributes ... ok
> Checking filters ... ok
> Annotation=getAnnotation(mart, featureType="TSS")

Best regards,

Julie


On 11/30/09 1:24 PM, "Khademul Islam" <khademul.islam@gmail.com> wrote:

> Hi,
> 
> the solution you described worked for archive biomart 51 (which is in archive
> list). But for 54, which is not in archive list (but I know how to define the
> "host" and "path" for biomart 54...........which actually I needed), I got
> following error. (may be you have seen that version 52 - 55 is not in the
> archive list)
> 
> This time I am not requesting to help me to fix this.............. just
> informing you this .........as the error itself telling to give it the mailing
> list !!!!!..........................because just for one particular version I
> don't wanna disturb you and take your time ...............as I can just
> download the annotation data and give it as input.... which is already working
> fine !!
> 
>> > mart=useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",
>> host="may2009.archive.ensembl.org <http://may2009.archive.ensembl.org/> ",
>> path="/biomart/martservice",archive=FALSE)
> Checking attributes ... ok
> Checking filters ... ok
>> > Annotation=getAnnotation(mart, featureType="TSS")
>                                                 V1
> 1                                           <html>
> 2 <head><title>504 Gateway Time-out</title></head>
> 3                           <body bgcolor="white">
> 4   <center><h1>504 Gateway Time-out</h1></center>
> 5                <hr><center>nginx/0.6.36</center>
> 6                                          </body>
> 7                                          </html>
> Error in getBM(c("ensembl_gene_id", "chromosome_name", "start_position",  : 
>   The query to the BioMart webservice returned an invalid result: the number
> of columns in the result table does not equal the number of attributes in the
> query. Please report this to the mailing list.
> 
> 
> thanks
> 
> Khademul
> 


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