[BioC] GOtools: argument is of length zero

[Paquet, Agnes]

Dear Balazs,

This error arises when you pass a vector or a list of vectors as argument to
ontoCompare or if the probeType argument doesn't match your data type. 

OntoCompare is expecting a list or a list of lists, so changing your
mdr.list into a list of lists may solve the problem. 

The probeType argument can be an affy chip or operon (for arrays with Operon
oligos).

Regards,

Agnes






 

-----Original Message-----
From: Dr_Gyorffy_Balazs [mailto:zsalab2 at yahoo.com] 
Sent: Monday, August 09, 2004 5:53 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] GOtools: argument is of length zero

Hi all,

I have tried to use the GOtools package, but I have
encountered following problem after running the ontoCompare
command: 

[1] "Starting ontoCompare..."
Error in if (ncol(results) == 0) results <- NA : 
        argument is of length zero


What is the reason for this? My original script is pasted
below.
THank you:
Balazs

---------------------------------------
mdr.table.5fu=read.table(?5FU.txt?, header=FALSE,
as.is=TRUE)
mdr.table.cisplatin=read.table(?cisplatin.txt?,
header=FALSE, as.is=TRUE)
mdr.table.cyclo=read.table(?cyclophosmphamid.txt?,
header=FALSE, as.is=TRUE)
mdr.list <- list(fu=mdr.table.5fu,
cisplatin=mdr.table.cisplatin,
cyclophosphamid=mdr.table.cyclo)
mdr.compared<-ontoCompare(mdr.list, probeType ="hgu133a",
method = "TIDS", plot = TRUE)

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