>> Subset replacement like this df['a','c2']<-3 depends on the position of row 'a' when 'c2' is a new column. Row 'a' first: > df1 <- DataFrame(c1=1:2,row.names=c("a","b")) > df1['a','c2'] <- 3 > df1 DataFrame with 2 rows and 2 columns c1 c2 <integer> <numeric> a 1 3 b 2 3 Row 'a' second: > df2 <- DataFrame(c1=1:2,row.names= rev( c("a","b") )) > df2['a','c2'] <- 3 > df2 DataFrame with 2 rows and 2 columns c1 c2 <integer> <numeric> b 1 NA a 2 3 FWIW, the latter - but not the former - agrees with "the 'DataFrame' behaves very similarly to 'data.frame'"(from the help page). > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.16.4 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] parallel_2.15.2 stats4_2.15.2

Hi Charles, Thanks for reporting the bug. Now fixed in 1.17.32 devel and 1.16.5 in release. Valerie library(RUnit) DF <- DataFrame("A"=1:5,row.names=letters[1:5]) df <- data.frame("A"=1:5,row.names=letters[1:5]) > checkIdentical(DF['a','B'] <- 1, df['a','B'] <- 1) [1] TRUE DF <- DataFrame("A"=1:5,row.names=letters[1:5]) df <- data.frame("A"=1:5,row.names=letters[1:5]) > checkIdentical(DF['c','B'] <- 1, df['c','B'] <- 1) [1] TRUE > sessionInfo() ... other attached packages: [1] RUnit_0.4.26 IRanges_1.16.5 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] parallel_2.15.1 stats4_2.15.1 On 02/09/2013 12:26 PM, Charles Berry wrote: >>> > > Subset replacement like this > > df['a','c2']<-3 > > depends on the position of row 'a' when 'c2' is a new column. > > > Row 'a' first: > >> df1 <- DataFrame(c1=1:2,row.names=c("a","b")) >> df1['a','c2'] <- 3 >> df1 > DataFrame with 2 rows and 2 columns > c1 c2 > <integer> <numeric> > a 1 3 > b 2 3 > > Row 'a' second: > >> df2 <- DataFrame(c1=1:2,row.names= rev( c("a","b") )) >> df2['a','c2'] <- 3 >> df2 > DataFrame with 2 rows and 2 columns > c1 c2 > <integer> <numeric> > b 1 NA > a 2 3 > > FWIW, the latter - but not the former - agrees with "the 'DataFrame' behaves > very similarly to 'data.frame'"(from the help page). > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IRanges_1.16.4 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] parallel_2.15.2 stats4_2.15.2 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >