Entering edit mode
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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