[BioC] Problem outputting normalized file

Jenny Drnevich drnevich at uiuc.edu
Mon Nov 10 21:14:01 MET 2003


I only work with Affymetrix arrays, so I didn't know about write.xls 
either! However, I found the following works to create a .csv file that can 
be read into SAS directly (I can't use Excel because with the probe-level 
data, there are more than Excel's limit of 65,536 rows). Try:

write.table(maM(swirl), file="swirlnorm.csv", quote=FALSE, sep=",", 
col.names=NA)

At 09:56 AM 11/10/2003 -0800, Jean Yee Hwa Yang wrote:
>Try
>
>write.table or
>
>write.xls(maM(swirl), file="swirlnorm.xls") ## A function in marrayInput.
>
>Jean
>
>
> > > write.table(swirl,"")
> > Error in as.data.frame.default(x[[i]], optional = TRUE) :
> >         can't coerce marrayRaw into a data.frame
> > > ls()
> > [1] "last.warning" "RGcol"        "swirl"        "swirl.norm"
> > "swirl.norm1"
> > [6] "swirl.norm2"  "swirl.normm"  "swirl.norms"  "tmp"
> > >
> >
> > (The "" is just for illustration. I get the same error message
> > when I output to a file, of course.)
> >
> > Also, when I try write.matrix, I get,
> >
> > > write.matrix(swirl.norm,"")
> > Error: couldn't find function "write.matrix"
> > >
> >
> > I would appreciate any suggestions as to how I can output the
> > normalized intensities. I regret bothering the group with
> > somethin so elementary. I have read the relevant parts of
> > "An Introduction to R", and R Data Import/Export, "The Basics
> > of S-Plus" and the on-line help for the write, write.table,
> > and write.matrix commands. I would expecially appreciate it,
> > if in addition to any specific suggestions, you could something
> > that I could read that deals with this topic.
> >
> > 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/
> >
> > "In slumberland there are 100 kinds of halavah and you
> > have to eat every one." -Rose Friedman, age 7
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
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Jenny Drnevich, Ph.D.
Department of Animal Biology
515 Morrill Hall
505 S Goodwin Ave
Urbana, IL 61801
USA

ph: 217-244-6826
fax: 217-244-4565
e-mail: drnevich at uiuc.edu



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