Question: ExpressionAtlas: download RPKM/TPM
0
gravatar for António Miguel de Jesus Domingues
15 months ago by
Germany

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?

Cheers

suppressMessages(library(ExpressionAtlas))

acc <- "E-ERAD-475"
allExps <- getAtlasData(acc)

sumexp <- allExps[[ acc ]]$rnaseq

assays(sumexp)

List of length 1
names(1): counts

 

SessionInfo()

embl tpm expressionatlas • 308 views
ADD COMMENTlink written 15 months ago by António Miguel de Jesus Domingues430
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