[BioC] Problem reading in files with marrayInput

[Jean Yee Hwa Yang]

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).
> 
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