[BioC] gcrma problem

[Zhijin Wu]

Since you have a special chip, will you check what "xy2i" function you
get with
  tmp <- get("xy2i", paste("package:", cdfpackagename, sep = ""))

Do you have NAs in pmIndex or subIndex?

You are right that the line
    tmp.exprs[pmIndex[subIndex]] = apm 
is  to assign the value from apm to tmp.exprs[pmIndex[subIndex]]. 

Jean

On Thu, 31 Mar 2005, Wenqiong Chen wrote:

> Hi, Jim and Zhijin:
> I found the problem with the probe package, and it turned out to be very
> much trivial! It is the problem with the quotation, in 
> >getProbePackage(disdiv712aprobe), the name of the probe package should
> be quoted! :-(
> 
> O.K, now, following each step in compute.affinities, I finally came to
> the "real" problem in the line
> > tmp.exprs[pmIndex[subIndex]] = apm
> Error: NAs are not allowed in subscripted assignments
> 
> I have checked vector "apm" and there is no NA, and the lengths of apm
> and tmp.exprs[pmIndex[subIndex]] are the same. Based on the code right
> before this line, the tmp.exprs[pmIndex[subIndex]] has all the NAs. Does
> this line try to assign the value from apm to
> tmp.exprs[pmIndex[subIndex]]?
> 
> Thanks a lot!
> Regards,
> wenqiong
> 
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: Thursday, March 31, 2005 11:24 AM
> To: Wenqiong Chen
> Cc: Bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] gcrma problem
> 
> Wenqiong Chen wrote:
> > Hi, Jim:
> > Thanks for debugging for me!
> > I tried the following commands and got exactly what you have expected.
> > Also, I tried everything in the unix system, and got exactly the same 
> > error message.
> > Wenqiong
> 
> Hmmm. What happens if you do this:
> 
> do.call("library", list("disdiv712acdf", .libPaths()[1]))
> do.call("library", list("disdiv712aprobe", .libPaths()[1]))
> search()
> 
> Does it list both of the packages after .GlobalEnv?
> 
> 
> 
> --
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> 
> 
> 
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