[BioC] DAVIDQuery

[Dan Tenenbaum]

cc'ing the DAVIDQuery maintainer.
I can reproduce this. The URL it's failing to download seems to be 
http://david.abcc.ncifcrf.gov/data/download/

which indeed gives me a 404 when I paste it into the browser, but that may be because I have not set the appropriate cookies, etc.

Dan


----- Original Message -----
> From: "Assa Yeroslaviz" <frymor at gmail.com>
> To: "Bioconductor mailing list" <bioconductor at r-project.org>
> Sent: Monday, February 3, 2014 12:27:02 PM
> Subject: [BioC] DAVIDQuery
> 
> Hi,
> 
> I am trying to analyze a set of flybase IDs with the DAVIDQuery
> package.  I
> would like to make a clustering analysis of a list of genes, but I
> keep
> getting some error messages.
> 
> I have a list of flybase IDs, eg.
> ids="FBgn0039239,FBgn0039337,FBgn0039350,FBgn0039356,FBgn0039494"
> With type
> type     <- "FLYBASE_GENE_ID"
> tool     <- "gene2gene"
> When I am running this command:
> result = DAVIDQuery(ids=ids, type =type, tool= tool, annot=NULL)
> 
> I am getting the following error message:
> 
> 
> 
> 
> 
> 
> *Error in file(file, "rt") : cannot open the connectionIn addition:
> Warning
> messages:1: In doTryCatch(return(expr), name, parentenv, handler) :
> Warning: downloadFileName is not found in reply html. 2: In
> file(file,
> "rt") : cannot open: HTTP status was '404 Not Found'*
> I tried to input the IDs as a character vector from an object, I
> tried to
> read a file as a data.frame, I even put them manually, but with no
> change.
> But when I am doing it with the same command and the affy IDs as an
> example
> ids =
> "33246_AT,32469_AT,1786_AT,32680_AT,1355_G_AT,37968_AT,33530_AT,31987_AT"
> type = "AFFYMETRIX_3PRIME_IVT_ID"
> tool     <- "gene2gene"
> 
> And this command
> result = DAVIDQuery(ids=ids, type =type, tool= tool, annot=NULL)
> 
> It works well.
> 
> What am I doing wrong or am I missing some important point about the
> package?
> Can't it work with FB IDs?
> 
> Runnning the same command with a diffferent tool works just fine.
> e.g.( DAVIDQuery(ids=ids, type =type, annot=NULL) with tools other
> than 1)
> 
> Thanks a lot for the information in advance.
> 
> Assa
> 
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> 
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