Personally I don't like this kind of behavior see "#*** and comments... It will surely catch someone out, will it use a rowname or a number , the joy of variable interpolation! Do I complain too much or is this worth a fix? > n<-8963 > fit2[8963,]$genes["ID"] ID 8963 106220736 ## ok that's what I wanted > fit2$genes[8961,"ID"] #** [1] "5050440" ## oops! > test<-fit2$genes > test[8963,] [1] "106220736" ## life is sane again, but now I need more caffeine! > > n<-8963 > fit2[n,]$genes["ID"] ID 8963 106220736 > fit2$genes[n,"ID"] ### Works as I would expect AGAIN [1] "106220736" > test<-fit2$genes > test[n,] [1] "106220736" > > fit2[8963,]$genes["ID"] ID 8963 106220736 > fit2$genes[8961,"ID"] [1] "5050440" > fit2$genes["8961","ID"] # Oh yes... now I get it! [1] "5050440" > fit2$genes[n,"ID"] [1] "106220736" > class(fit2) [1] "MArrayLM" attr(,"package") [1] "limma" > sessionInfo() R version 2.7.1 RC (2008-06-16 r45949) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.14.5 > Cheers Paul [[alternative HTML version deleted]]

Hi Paul, you've unearthed the terror that is using numerical ID's as rownames! As a rule, if I have numerical rownames, then I always refer to them using a quoted number - ie a character, eg rma["12356",], or programatically using the as.character wrapper, eg: psID <- 12345 rma[as.character(psID),] I did not realise the error snuck in at your 2nd line (fit2$genes[8961,"ID") This is an important issue to watch out for, for those using new generation affy arrays, where the probesetID's/transcript cluster ID's or whatever they're now called are numbers. cheers, Mark On 26/06/2008, at 5:33 PM, Paul Leo wrote: > Personally I don't like this kind of behavior see "#*** and > comments... > It will surely catch someone out, will it use a rowname or a number , > the joy of variable interpolation! > Do I complain too much or is this worth a fix? > >> n<-8963 >> fit2[8963,]$genes["ID"] > ID > 8963 106220736 ## ok that's what I wanted >> fit2$genes[8961,"ID"] #** > [1] "5050440" ## oops! >> test<-fit2$genes >> test[8963,] > [1] "106220736" ## life is sane again, but now I need more caffeine! >> >> n<-8963 >> fit2[n,]$genes["ID"] > ID > 8963 106220736 >> fit2$genes[n,"ID"] ### Works as I would expect AGAIN > [1] "106220736" >> test<-fit2$genes >> test[n,] > [1] "106220736" >> >> fit2[8963,]$genes["ID"] > ID > 8963 106220736 >> fit2$genes[8961,"ID"] > [1] "5050440" >> fit2$genes["8961","ID"] # Oh yes... now I get it! > [1] "5050440" >> fit2$genes[n,"ID"] > [1] "106220736" > > >> class(fit2) > [1] "MArrayLM" > attr(,"package") > [1] "limma" >> sessionInfo() > R version 2.7.1 RC (2008-06-16 r45949) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] limma_2.14.5 >> > > > Cheers > Paul > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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