[BioC] gcrma problem

[James MacDonald]

You could probably just switch the order of the variables in the call to
match(). If the length of the first variable is shorter than the second,
there will not be any NAs produced. I don't think this will be a problem
since you are just trying to get the set of probes that are common to
both packages.

HTH,

Jim



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
>>> "Wenqiong Chen" <wenchen at diversa.com> 04/01/05 1:58 PM >>>
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!
Regards, 
wenqiong



-----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]]. 

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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