Dear list, I'm creating an R package to store RNA-seq data of a somewhat large project in which I'm involved.
One of the initial goals is to compare different pre-processing pipelines, hence I have multiple expression matrices corresponding to the same samples. The SummarizedExperiment class seems a good candidate, since I have multiple expression matrices with the same rowData and colData information. I have several sample-specific variables that I want to store with the object, namely, experimental information (e.g., batch, date, experimental condition, ...) and sample quality (e.g., proportion of aligned reads, total duplicate reads, etc...). Of course, I can always create one big data frame concatenating the two (experimental info + sample quality), but it seems that both conceptually and practically, it might be useful to have two separate data frames. Since this seems somewhat a reasonably standard type of information that one would want to carry on, I was wondering if it would be possible / useful to allow the user to have multiple data.frames in the colData slot of SummarizedExperiment. Best, Davide [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel