Dear all, first of all I apologise if this is a silly question. I am using R version 1.7.1 Beta I am trying to create objects of class marrayinfo following the example on the marrayInfo documentation for a set of 6 cDNA chips. > mydata.layout Array layout: Object of class marrayLayout. Total number of spots: 12288 Dimensions of grid matrix: 12 rows by 4 cols Dimensions of spot matrices: 16 rows by 16 cols Currently working with a subset of 12288 spots. Control spots: Notes on layout: No Input File I have created a text file called "samples.txt" following the format of SwirlSample.txt as follows # of slide Names experiment Cy3 experiment Cy5 1 sample1.txt control treated 1 2 sample2.txt control treated 1 3 sample3.txt control treated 1 4 sample4.txt control treated 2 5 sample5.txt control treated 2 6 sample6.txt control treated 2 and then tried to load it... and got the following error: > mydata.samples<- read.marrayInfo(file.path(datadir, "samples.txt")) Error in paste.default("Invalid object for slot \"", slotName, "\" in class\"", : Object "slotName" not found Is there anything I am missing? Thanks in advance David

Hi David, Sorry, this is a bug in marray* packages. There is a fix if you download the marrayClasses 1.2.1 (developmental version). http://www.bioconductor.org/repository/devel/package/html/marrayClasse s.html I am in process of putting the bug fix on the release version. Cheers Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Division of Biostatistics, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Tue, 8 Jul 2003 kfbargad@lg.ehu.es wrote: > Dear all, > > first of all I apologise if this is a silly question. > > I am using R version 1.7.1 Beta > > I am trying to create objects of class marrayinfo following the > example on the marrayInfo documentation for a set of 6 cDNA chips. > > > mydata.layout > Array layout: Object of class marrayLayout. > > Total number of spots: 12288 > Dimensions of grid matrix: 12 rows by 4 cols > Dimensions of spot matrices: 16 rows by 16 cols > > Currently working with a subset of 12288 spots. > > Control spots: > > > Notes on layout: > No Input File > > I have created a text file called "samples.txt" following the format > of SwirlSample.txt as follows > > # of slide Names experiment Cy3 experiment Cy5 > 1 sample1.txt control treated 1 > 2 sample2.txt control treated 1 > 3 sample3.txt control treated 1 > 4 sample4.txt control treated 2 > 5 sample5.txt control treated 2 > 6 sample6.txt control treated 2 > and then tried to load it... and got the following error: > > > mydata.samples<- read.marrayInfo(file.path(datadir, "samples.txt")) > Error in paste.default("Invalid object for slot \"", slotName, "\" in > class\"", : > Object "slotName" not found > > Is there anything I am missing? > > Thanks in advance > > David > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Thanks a lot Jean, it works fine now! I now have another error when reading in my quantarray files using the read.marrayRaw function. This is what I do: > fnames<-dir(path=datadir, pattern ="^[sample]",full.names=TRUE) > fnames [1] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample1.tx t" [2] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample2.tx t" [3] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample3.tx t" [4] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample4.tx t" [5] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample5.tx t" [6] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample6.tx t" > mydata.raw<-read.marrayRaw(fnames, path=NULL, name.Gf = "ch2 Intensity", + name.Gb = "ch2 Background", name.Rf = "ch1 Intensity", name.Rb = "ch1 Background", + layout = mydata.layout, gnames = mydata.names, targets = samples, skip = 12331) [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample1.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample2.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample3.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample4.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample5.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample6.txt" Error in "maTargets<-"(*tmp*, value = targets) : No direct or inherited method for function "maTargets<-" for this call In addition: Warning messages: 1: number of items read is not a multiple of the number of columns 2: number of items read is not a multiple of the number of columns 3: number of items read is not a multiple of the number of columns 4: number of items read is not a multiple of the number of columns 5: number of items read is not a multiple of the number of columns 6: number of items read is not a multiple of the number of columns > Why do I get this error? and what does the warning mean? We have each oligonucleotide sequence spotted two times on the chip. How does the function handle duplicate spots? Thanks a lot David > Hi David, > > Sorry, this is a bug in marray* packages. There is a fix if you download > the marrayClasses 1.2.1 (developmental version). > http://www.bioconductor.org/repository/devel/package/html/marrayClasse s html > I am in process of putting the bug fix on the release version. > > Cheers > > Jean > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Jean Yee Hwa Yang jean@biostat.ucsf.edu > Division of Biostatistics, Tel: (415) 476-3368 > University of California, Fax: (415) 476-6014 > 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > On Tue, 8 Jul 2003 kfbargad@lg.ehu.es wrote: > > > Dear all, > > > > first of all I apologise if this is a silly question. > > > > I am using R version 1.7.1 Beta > > > > I am trying to create objects of class marrayinfo following the > > example on the marrayInfo documentation for a set of 6 cDNA chips. > > > > > mydata.layout > > Array layout: Object of class marrayLayout. > > > > Total number of spots: 12288 > > Dimensions of grid matrix: 12 rows by 4 cols > > Dimensions of spot matrices: 16 rows by 16 cols > > > > Currently working with a subset of 12288 spots. > > > > Control spots: > > > > > > Notes on layout: > > No Input File > > > > I have created a text file called "samples.txt" following the format > > of SwirlSample.txt as follows > > > > # of slide Names experiment Cy3 experiment Cy5 > > 1 sample1.txt control treated 1 > > 2 sample2.txt control treated 1 > > 3 sample3.txt control treated 1 > > 4 sample4.txt control treated 2 > > 5 sample5.txt control treated 2 > > 6 sample6.txt control treated 2 > > and then tried to load it... and got the following error: > > > > > mydata.samples<- read.marrayInfo(file.path (datadir, "samples.txt")) > > Error in paste.default("Invalid object for slot \"", slotName, "\" in > > class\"", : > > Object "slotName" not found > > > > Is there anything I am missing? > > > > Thanks in advance > > > > David > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >

David, Re: what does the warning mean? Are they all copies of the same file? I think the warning is because as scan reads in the list of data it is recycling the elements (number of columns) in the vector h in the read.marrayRaw code completely scrambling your data. dat <- scan(f, quiet = TRUE, what = h, sep = sep, skip = skip + 1, quote = quote, ...) This could be caused by having just one less/extra tab somewhere in your data files either in your data rows or the colnames header row itself. Skip =12331 is a lot of rows to skip is this right? marcus Thanks a lot Jean, it works fine now! I now have another error when reading in my quantarray files using the read.marrayRaw function. This is what I do: > fnames<-dir(path=datadir, pattern ="^[sample]",full.names=TRUE) > fnames [1] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample1.tx t" [2] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample2.tx t" [3] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample3.tx t" [4] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample4.tx t" [5] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample5.tx t" [6] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample6.tx t" > mydata.raw<-read.marrayRaw(fnames, path=NULL, name.Gf = "ch2 Intensity", + name.Gb = "ch2 Background", name.Rf = "ch1 Intensity", name.Rb = "ch1 Background", + layout = mydata.layout, gnames = mydata.names, targets = samples,s kip = 12331) [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample1.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample2.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample3.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample4.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample5.txt" [1] "Reading C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample6.txt" Error in "maTargets<-"(*tmp*, value = targets) : No direct or inherited method for function "maTargets<-" for this call In addition: Warning messages: 1: number of items read is not a multiple of the number of columns 2: number of items read is not a multiple of the number of columns 3: number of items read is not a multiple of the number of columns 4: number of items read is not a multiple of the number of columns 5: number of items read is not a multiple of the number of columns 6: number of items read is not a multiple of the number of columns > Why do I get this error? and what does the warning mean? We have each oligonucleotide sequence spotted two times on the chip. How does the function handle duplicate spots? Thanks a lot David ______________________________________________________ The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail.

Dear Marcus and Jean, thanks for your help. Jean, regarding your suggestions, I have tried them and this is what I get: > maLayout(mydata.raw)<-mydata.layout Error: Object "mydata.raw" not found > maGnames(mydata.raw)<-mydata.names Error: Object "mydata.raw" not found > class(samples) [1] "genericFunction" > maTargets(mydata.raw)<-samples Error: Object "mydata.raw" not found Marcus, the six files are six different QuantArray files. They are tab delimited text files and the first part of the file (the first 12331 rows) are information we don?t use. We use the second half of the file where the intensities for each channel are shown. > David, > Re: what does the warning mean? > > Are they all copies of the same file? > > I think the warning is because as scan reads in the list of data it is recycling the elements (number of columns) in the vector h in the read.marrayRaw code completely scrambling your data. > > dat <- scan(f, quiet = TRUE, what = h, sep = sep, skip = skip + > 1, quote = quote, ...) > > This could be caused by having just one less/extra tab somewhere in your data files either in your data rows or the colnames header row itself. > > Skip =12331 is a lot of rows to skip is this right? > > > marcus > > >