[BioC] three more questions

[Wolfgang Huber]

Hi Zhao,
all of your questions can be answered by looking at the R documentation.

> Quesion 1: Is there any way to run Bioconductor functions in command line,
> e.g. under DOS enviroment, without open Bioconductor application and without
> showing the prompt (>) of R.

Yes. There is a batch mode for R. See:

 Rcmd batch --help

on the DOS command line, and the "An Introduction to R" on 
www.r-project.org

Alternatively, you can call shell (DOS, unix) commands from within R 
using the system() function

> Question 2: In the output text file (e.g. after rma analysis), is there any
> way to add additional text information in that file? e.g. can
> 'write.exprs(eset, file="mydata.txt")' write more information into
> "mydata.txt"?
On the R command line, type 

> ? file.append
> ? cat

The cat() function with append=TRUE may be what you want.

> Question 3: If you open the output of rma analysis text file with excel, the
> column title (Affymetrix cel file name) and the column content are not lined
> up correctly. The title should be moved one column to the right. Is there
> any way to to change this?

This is what I think is a bug in the write.table() function of R. It could 
be circumvented my modifying the code in the affy package that uses it 
(Ben? Rafael?)

Best regards
Wolfgang