I am trying to run RMA algorithm of more than 256 arrays. One problem I encoutered was that the excel file (output file) allows maximal 256 columns. I then named the output file as "output.csv" or "output.txt". No one of them worked for me when more than 256 arrays were processed. The algorithm was run but there was no output file. I ensure that it is not a problem of any files because as I split the all arrays into two group, each group could be processed. It seems that RMA has a global normalization with all arrays. If this is true, how can I preprocess more than 256 arrays with RMA algorithm. Hairong

It is not clear what your question is but it could be either 1) Excel cannot open a file with more than 256 columns OR 2) I cannot run RMA on more than 256 columns If it is 1), then perhaps you could write the final output it into 2 or more separate files. Or you could try other spreadsheet solutions such as open office. But why would you want to do this because looking at expression measure alone provides little information. R can certainly handle files with more than 256 columns, so I only print out the final results. If it is 2), then search for "many RMA" or "large amount of slides" in http://files.protsuggest.org/cgi-bin/biocond.cgi. Some detail of the computing power available to you and approximate number of arrays could narrow down some of the suggestions you find here. You mentioned that the "Algorithm was run but there was no output" but was the algorithm _successfully_ run ? Check for error messages. Regards, Adai On Mon, 2004-09-06 at 17:48, Hairong Wei wrote: > I am trying to run RMA algorithm of more than 256 arrays. One problem I > encoutered was that the excel file (output file) allows maximal 256 columns. > I then named the output file as "output.csv" or "output.txt". No one of > them worked for me when more than 256 arrays were processed. The algorithm > was run but there was no output file. I ensure that it is not a problem > of any files because as I split the all arrays into two group, each group > could be processed. > > It seems that RMA has a global normalization with all arrays. If this is > true, how can I preprocess more than 256 arrays with RMA algorithm. > > Hairong > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

I am trying to run RMA algorithm of more than 256 arrays. One problem I encoutered was that the excel file (output file) allows maximal 256 columns. I then named the output file as "output.csv" or "output.txt". No one of them worked for me when more than 256 arrays were processed. The algorithm was run but there was no output file. I ensure that it is not a problem of any files because as I split the all arrays into two group, each group could be processed. It seems that RMA has a global normalization with all arrays. If this is true, how can I preprocess more than 256 arrays with RMA algorithm. Hairong