[BioC] gcrma problem

Wenqiong Chen wenchen at diversa.com
Fri Apr 1 20:58:43 CEST 2005

You are right, there are NAs in subIndex. So here are the numbers:
>length(pmIndex) = 248102
>tmp(p$x, p$y) = 251035
So when executing the line: subIndex<-match(tmp(p$x, p$y), pmIndex) NAs
got created.
The problem did not come with the Affy chip, rather I should be the one
to be blamed, although I can justified myself why I did this. The chip
was designed a few years ago and for these couple of years, of course we
have gone through a number of re-annotation and ORF calling. To reflect
the changes, I have modified the cdf file, which includes deleting
probes, reassigning old probes to new genes, etc. As a consequence, some
of the probes in the probe sequence files are no use. Originally I
thought that as far as the sequences for all the probes on the cdf file
are there, things should be O.K, but apparently I am wrong. 
Is there anything we can do by re-scripting the code? I guess it
probably makes more sense to you by simply modifying my probe sequence
file, but it is quite a bit of work.
Thanks a lot for your time!

-----Original Message-----
From: Zhijin Wu [mailto:zwu at jhsph.edu] 
Sent: Friday, April 01, 2005 6:28 AM
To: Wenqiong Chen
Cc: Bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] gcrma problem

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]]. 


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
> > 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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