This probably happened because the object returned from justRMA changed from a exprSet to an ExpressionSet and that these two classes have different coercion rules But for both class exprs(OBJECT) returns the same matrix - hence write.exprs is stable. So to summarize, my guess is that it has to do with changes in the underlying representation. Kasper On Mar 7, 2008, at 12:00 PM, James W. MacDonald wrote: > > > Balasubramanian Ganesan wrote: >> Dear all >> I am running R-2.6.2 on a PowerPC PowerBook-G4. >> I am using the following method to normalize my data. >> >>> library(affy) >>> eset=justRMA() >> >> I used two different ways of writing out the eset data. >>> write.table(eset,file="abc.txt",sep="\t") # produces a table with >> probe IDs as cols and sample names as rows (order of data is >> transposed) >> >> But if I use >>> write.exprs(eset,file="abc2.txt") # produces a table with probe IDs >> as rows and sample names as col headers, which is what we want. >> >> Why do I see this discrepancy? I have always used "Write.table" in >> the past and has always worked for me upto R-2.5. I started having >> this issue only with R-2.6 and have it with both versions of 2.6. > > You get this discrepancy because write.table() isn't designed to use > an > S4 object. From ?write.table > > Arguments: > > x: the object to be written, preferably a matrix or data frame. > If not, it is attempted to coerce 'x' to a data frame. > > So by using write.table() rather than the function specifically > written > to do what you want, you are assuming that the coercion of an > ExpressionSet to data.frame will end up doing what you expect. > Evidently > it did so in the past, but there was never any guarantee that this > would > work, and evidently it no longer does. > > Best, > > Jim > > >> >> Balasubramanian Ganesan >> Research Assistant Professor >> Center for Integrated BioSystems >> Utah State University >> 4700 Old Main Hill >> Logan UT 84322 >> balag at cc.usu.edu >> >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > 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