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 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?

Just as I gave this msg I find a simliar issue in May 2002 archive About a similar problem and the solution ... [BioC] Question about affy Rafael A. Irizarry rafa@jhu.edu Wed, 15 May 2002 11:00:33 -0400 (EDT) this is a bug. we assume that you will provide phenoData (look at the help file or the Biobase description). if you have phenotypic data and it has more than 2 covariantes add it. that will solve your problem. otherwise, while we fix it, here is a work around So I will give it a shot and see if it works ... Thanks Shyam -----Original Message----- From: Sundaram, Shyam (NIH/CIT) Sent: Wednesday, November 06, 2002 1:26 PM To: Bioconductor (E-mail) Subject: [BioC] Affy : checkSlotAssignment() Error 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 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

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 -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+

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 -- +--------------------------------------------------------------------- ------ + | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------ +