[BioC] Affy : checkSlotAssignment() Error

Sundaram, Shyam (NIH/CIT) shyam@mail.nih.gov
Wed, 6 Nov 2002 14:02:28 -0500


The following is  a screen dump using the traceback() and debug() as
suggested. I will also step thru using the debug and see if I can locate the
exact problem ...
Thanks

>d<-ReadAffy()
reading CDF file
processing information
reading 1 CEL files.
preparing probe level object

> e<-express(d)
Normalizing Data
Error in checkSlotAssignment(object, name, value) :
        Value supplied is not valid for slot "pm", is(value, "matrix") is
not TRUE


> traceback()
10: stop(paste("Value supplied is not valid for slot \"", name, "\",
is(value, \""
,
        slot, "\") is not TRUE", sep = ""))
9: checkSlotAssignment(object, name, value)
8: "slot<-"(object, name, TRUE, value)
7: "@<-"(*tmp*, pm, value = value)
6: "pm<-"(*tmp*, value = x[1:n, ])
5: normalize.Plob.quantiles(object, ...)
4: do.call(method, alist(object, ...))
3: .local(object, ...)
2: normalize(object, method = normalize.method, span = span, choose.subset =
choose.subset,
       subset.size = subset.size, verbose = verbose, maxit = maxit)
1: express(d)


Debugging the process within the normalize() method the following is the
screen dump..
 e<-express(d)
Normalizing Data
debugging in: normalize(object, method = normalize.method, span = span,
choose.sub
set = choose.subset,
    subset.size = subset.size, verbose = verbose, maxit = maxit)
debug: standardGeneric("normalize")
Browse[1]> dim(pm(object))
[1] 247965      1
Browse[1]> object
Plob object
CDF used=HG-U133A.CDF
number of chips=1
number of genes=22283
number of probe pairs=247965
annotation=
description=
notes=
size of chip=712x712
chip names=
BT_100802_OCI_LY19b1_1_U133A


-----Original Message-----
From: Robert Gentleman [mailto:rgentlem@jimmy.harvard.edu]
Sent: Wednesday, November 06, 2002 1:48 PM
To: Sundaram, Shyam (NIH/CIT)
Cc: Bioconductor (E-mail)
Subject: Re: [BioC] Affy : checkSlotAssignment() Error


On Wed, Nov 06, 2002 at 01:26:15PM -0500, Sundaram, Shyam (NIH/CIT) wrote:
> Hi:
> Thanks in advance for helping.
> I was able to load successfully the "HG-U133A" CEL and CDF file through
the
> ReadAffy() method into a "plob" object. When I tried to convert it to the
> exprSet using the express() function I was faced with the following error
> message.
> Normalizing Data
> Error in checkSlotAssignment(object, name, value) : 
>         Value supplied is not valid for slot "pm", is(value, "matrix") is
> not TRUE

 Hi,
  could you rerun the problem to this point and then (before doing
  anything else) in R do
  
  traceback()

  This should tell us where you are.
  You could then use the debug function in R to try and track down
  just what the problem is. 
  Basically there is some problem and the pm matrix has not been
  computed. To diagnose the exact problem we need to know a bit more.


> To make sure the cel,cdf files are loaded properly I tried to load them
> through the read.celfile, read.cdffile methods and they seem to do so with
> out errors.
> Any suggestions on what might be the cause of the problem?
> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

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