[BioC] Problem reading in files with marrayInput Ignore previous response

Jean Yee Hwa Yang jean at biostat.ucsf.edu
Wed Nov 5 17:54:33 MET 2003


Hi Richard,

Could you place array1.5.spot and array1.6.spot online somewhere for me to
download or e-mail the two files for me to take a look.

Cheers

Jean

> #######################################################################
> > fnames <-dir(path=datadir,pattern=paste("*","spot",sep="\."))[1:6]
> > array1.raw <- read.Spot(fnames, path=datadir)
> [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot"
> [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot"
> [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot"
> [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot"
> [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot"
> [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot"
> Warning messages:
> 1: number of items read is not a multiple of the number of columns
> 2: number of rows of result
>         is not a multiple of vector length (arg 2) in: cbind(Gf,
> as.numeric(dat[[name.Gf]]))
> 3: number of rows of result
>         is not a multiple of vector length (arg 2) in: cbind(Gb,
> as.numeric(dat[[name.Gb]]))
> 4: number of rows of result
>         is not a multiple of vector length (arg 2) in: cbind(Rf,
> as.numeric(dat[[name.Rf]]))
> 5: number of rows of result
>         is not a multiple of vector length (arg 2) in: cbind(Rb,
> as.numeric(dat[[name.Rb]]))
> >
> ##################################################################
> As far as I can see, my array1 spot files are comparable to the
> swirl files, except that they contain a few extra columns.
> The last column in the swirl files are badspot. The array1 files have
> two columns to the right of badspot: nominal.center.row
> nominal.center.col. Should that make a difference?
> 
> Thanks and best wishes,
> Rich
> 
> On Mon, 3 Nov 2003, Jean Yee Hwa Yang wrote:
> 
> > Hi Richard,
> >
> > Look at the examples in help(read.marrayRaw)
> > Copy and paste the whole set of examples and see if it works.
> > If so, it's possible something is not right with the spot files.
> >
> > Try simply reading the data in:
> > array1.raw <- read.Spot(fnames, path=datadir)
> > and see if it works.
> >
> > Cheers
> >
> > Jean
> >
> > > > array1.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "Gmean",
> > > +       name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR",
> > > +       layout = array1.layout, gnames = array1.gnames, targets =
> > > array1.samples)
> > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot"
> > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot"
> > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot"
> > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot"
> > write.table(data.frame(AnnA[DEList,],AllData), file=file.path(resdir,
> > "AllData.xls"),sep="\t", row.names=FALSE)>
> > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot"
> > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot"
> > > Warning messages:
> > > 1: number of items read is not a multiple of the number of columns
> > > 2: number of rows of result
> > >         is not a multiple of vector length (arg 2) in: cbind(Gf,
> > > as.numeric(dat[[name.Gf]]))
> > > 3: number of rows of result
> > >         is not a multiple of vector length (arg 2) in: cbind(Gb,
> > > as.numeric(dat[[name.Gb]]))
> > > 4: number of rows of result
> > >         is not a multiple of vector length (arg 2) in: cbind(Rf,
> > > as.numeric(dat[[name.Rf]]))
> > > 5: number of rows of result
> > >         is not a multiple of vector length (arg 2) in: cbind(Rb,
> > > as.numeric(dat[[name.Rb]]))
> > > >
> > >
> > > ##############################################################
> > > Thanks and best wishes,
> > > Rich
> > > ------------------------------------------------------------
> > > Richard A. Friedman, PhD
> > > Associate Research Scientist
> > > Herbert Irving Comprehensive Cancer Center
> > > Oncoinformatics Core
> > > Lecturer
> > > Department of Biomedical Informatics
> > > Box 95, Room 130BB or P&S 1-420C
> > > Columbia University
> > > 630 W. 168th St.
> > > New York, NY 10032
> > > (212)305-6901 (5-6901) (voice)
> > > friedman at cancercenter.columbia.edu
> > > http://cancercenter.columbia.edu/~friedman/
> > >
> > > "Everybody is going to do their book reports on Harry Potter.
> > > I'm going to do mine on 'Red Planet'." -Isaac Friedman, age 13
> > > (I know I said "no more Isaac quotes", but I couldn't resist that one).
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > >
> >
> >
> 
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist
> Herbert Irving Comprehensive Cancer Center
> Oncoinformatics Core
> Lecturer
> Department of Biomedical Informatics
> Box 95, Room 130BB or P&S 1-420C
> Columbia University
> 630 W. 168th St.
> New York, NY 10032
> (212)305-6901 (5-6901) (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
> 
> "In slumberland there are 100 kinds of halavah and you
> have to eat every one." -Rose Friedman, age 7
>



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