I downloaded data for an RNA-seq experiment using the ExpressionAtlas package - very very straightforward by the way. Sadly the data contains only the raw counts from said experiment, whereas my expectation was that one would also get access to the pre-calculated RPKM/TPM since these are available for download in the Expression Atlas site. Of course I could simply download the TPM data manually and take it from there (which I did), but for the sake of reproducibility I was wondering if this data is also accessible using the package. Did I miss it?
suppressMessages(library(ExpressionAtlas)) acc <- "E-ERAD-475" allExps <- getAtlasData(acc) sumexp <- allExps[[ acc ]]$rnaseq assays(sumexp) List of length 1 names(1): counts