R help - Jan 2006 - Loading Excel file into Limma

Dear mailing group,

  This is my first time here. Glad to have this resource!

  I am currently trying to load an Excel file into R (limma package loaded) 
using the source(*name of directory*) command, but it cannot open the file. 
I renamed the file as .R and .RData, to no avail. The Excel data contains 
one gene name per row and about 100 data points per gene (columns).

  I am only used to loading preprepared microarray data with all the t's 
crossed and i's dotted, with the read.maimages command. Can anyone help me 
out with this silly-sounding "challenge"?

  Sincerely - in the truest sense - 

Norman Goodacre

well, I don't know anything about the limma package and I might be 
misunderstanding your apparently simple question

What I do for excel files is the following:
1. I save a copy of the file as .csv (comma separated values) in the 
working directory. This format allows you work perfectly with the file in 
excel.
2. open in R using:

 > read.csv("filename.csv")

Hope it helps



At 12:48 12/01/2006, you wrote:
>Dear mailing group,
>
>   This is my first time here. Glad to have this resource!
>
>   I am currently trying to load an Excel file into R (limma package loaded)
>using the source(*name of directory*) command, but it cannot open the file.
>I renamed the file as .R and .RData, to no avail. The Excel data contains
>one gene name per row and about 100 data points per gene (columns).
>
>   I am only used to loading preprepared microarray data with all the
t's
>crossed and i's dotted, with the read.maimages command. Can anyone help
me
>out with this silly-sounding "challenge"?
>
>   Sincerely - in the truest sense -
>
>Norman Goodacre
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
Ahimsa Campos Arceiz
The University Museum,
The University of Tokyo
Hongo 7-3-1, Bunkyo-ku,
Tokyo 113-0033
phone +81-(0)3-5841-2824
cell +81-(0)80-5402-7702

no idea bout limma. but you could load excel data into R by using rodbc.
here is a sample code and hope it helpful.

library(RODBC);

###########################################################
# 1. READ DATA FROM EXCEL INTO R #
###########################################################
xlsConnect<-odbcConnectExcel("C:\\temp\\demo.xls");
demo<-sqlFetch(xlsConnect, "Sheet1");
odbcClose(xlsConnect);
rm(demo);


On 12 Jan 2006 03:48:26 +0000, N. Goodacre <ng296@cam.ac.uk>
wrote:
>
> Dear mailing group,
>
>   This is my first time here. Glad to have this resource!
>
>   I am currently trying to load an Excel file into R (limma package
> loaded)
> using the source(*name of directory*) command, but it cannot open the
> file.
> I renamed the file as .R and .RData, to no avail. The Excel data contains
> one gene name per row and about 100 data points per gene (columns).
>
>   I am only used to loading preprepared microarray data with all the
t's
> crossed and i's dotted, with the read.maimages command. Can anyone help
me
> out with this silly-sounding "challenge"?
>
>   Sincerely - in the truest sense -
>
> Norman Goodacre
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>


--
WenSui Liu
(http://statcompute.blogspot.com)
Senior Decision Support Analyst
Health Policy and Clinical Effectiveness
Cincinnati Children Hospital Medical Center

	[[alternative HTML version deleted]]

R won't read an Excel sheet directly.  You need to export it, saving it as a
CSV or tab delimited file.  You can then import using read.table.  The entire 
path and file have to be in double-quotes as well.  Try ?read.table for more 
info.

JWD

On Wednesday 11 January 2006 19:48, N. Goodacre wrote:
> Dear mailing group,
>
>   This is my first time here. Glad to have this resource!
>
>   I am currently trying to load an Excel file into R (limma package loaded)
> using the source(*name of directory*) command, but it cannot open the file.
> I renamed the file as .R and .RData, to no avail. The Excel data contains
> one gene name per row and about 100 data points per gene (columns).
>
>   I am only used to loading preprepared microarray data with all the
t's
> crossed and i's dotted, with the read.maimages command. Can anyone help
me
> out with this silly-sounding "challenge"?
>
>   Sincerely - in the truest sense -
>
> Norman Goodacre
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html

another options: use read.xls in gdata pcakges if you have installed
perl in you machine .

12 Jan 2006 03:48:26 +0000, N. Goodacre <ng296 at
cam.ac.uk>:
> Dear mailing group,
>
>   This is my first time here. Glad to have this resource!
>
>   I am currently trying to load an Excel file into R (limma package loaded)
> using the source(*name of directory*) command, but it cannot open the file.
> I renamed the file as .R and .RData, to no avail. The Excel data contains
> one gene name per row and about 100 data points per gene (columns).
>
>   I am only used to loading preprepared microarray data with all the
t's
> crossed and i's dotted, with the read.maimages command. Can anyone help
me
> out with this silly-sounding "challenge"?
>
>   Sincerely - in the truest sense -
>
> Norman Goodacre
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>

--
伝伷伻佡伖侒
Deparment of Sociology
Fudan University