[BioC] Error creating marrayInfo

[kfbargad at lg.ehu.es]

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/marrayClasses
html
> I am in process of putting the bug fix on the release version.
> 
> Cheers
> 
> Jean
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>  Jean Yee Hwa Yang			 jean at 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 at 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 at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
>