[BioC] Problem outputting normalized file

[Jenny Drnevich]

Besides the vignettes, go to the package listing page and click on any of 
the packages. Above the source and Win32 download links, there is a link to 
Function Descriptions. This lists the functions in the package and a brief 
description of each. Then I usually query within R (?write.xls) to find out 
more details.

However, I also would like to know if there is a comprehensive list of 
function descriptions somewhere, because it's too tedious to look through 
all of them to see what functions in other packages could be useful for my 
Affy data analysis.

Cheer,
Jenny


At 02:17 PM 11/10/2003 -0500, you wrote:
>Jean,
>
>         Thank you very much. As best I can see write.xls was not covered 
> in the "Introduction to marrayInput". It is also not discussed  in the 
> on-line help under marrayInput. Is there some way I could have learned 
> about this function short of querying the news group? I ask in case there 
> is a source of documentation that I am apparently missing.
>
>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
>
>
>On Monday, November 10, 2003, at 12:56 PM, 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
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

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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