Thanks a lot for answering my previous questions. It helps a lot. I have three more questions. 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. 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"? 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? Thanks a lot. Po

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

> -----Original Message----- > From: Wolfgang Huber [mailto:whuber@jimmy.harvard.edu] > > 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?) This isn't a 'bug' per se. From the write.table documentation: Normally there is no column name for a column of row names. If `col.names=NA' a blank column name is added. This can be used to write CSV files for input to spreadsheets. This option should probably be added to the appropriate call to write.table. -Greg > > Best regards > Wolfgang > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > LEGAL NOTICE\ Unless expressly stated otherwise, this message is... [[dropped]]