I looking for ways to do RMA on only a subset of probesets on a microarray. I use the following code to get the data from cel files. ####### library(oligo) cel_files = list.celfiles('data', full.names=TRUE) data=read.celfiles(cel_files) ####### I can get the raw data by the following code. Then, I can take a subset of it and assige it back. ### uncorrected_probeset_data = get('exprs', data at assayData) #### However, I believe that 'rma()' should call, for example, "pd.huex.1.0.st.v2" package. Just changing 'exprs' in data at assayData would not be sufficient. I'm wondering how to modify variables in the packages called by 'rma()'. ##### eset=rma(data) ########

Hi Peng, This is not yet an implemented feature. If you really want to do that yourself, you can use the features in the preprocessCore package. Is there an specific reason rma() is not sufficient for what you need? Also, what do you plan to use to create the subset you refer to? (Asking this because I'm willing to put some effort on implementing such thing some time soon) Thank you, b On Oct 14, 2009, at 11:29 AM, Peng Yu wrote: > I looking for ways to do RMA on only a subset of probesets on a > microarray. I use the following code to get the data from cel files. > > ####### > library(oligo) > cel_files = list.celfiles('data', full.names=TRUE) > data=read.celfiles(cel_files) > ####### > > I can get the raw data by the following code. Then, I can take a > subset of it and assige it back. > > ### > uncorrected_probeset_data = get('exprs', data at assayData) > #### > > However, I believe that 'rma()' should call, for example, > "pd.huex.1.0.st.v2" package. Just changing 'exprs' in data at assayData > would not be sufficient. I'm wondering how to modify variables in the > packages called by 'rma()'. > > ##### > eset=rma(data) > ######## > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor