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

Richard Friedman friedman at cancercenter.columbia.edu
Wed Nov 5 17:40:26 MET 2003


Dear Jean and Everybody,

	Please ignore my previous response. The test with the
Swirl data works fine. I had put the data in a subdirectory.

When I try the second command filesthat you
suggested (after moving the swirl.?.spot files out of data ) I get
#######################################################################
> 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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