[BioC] Summarized Experiments - Combine

Valerie Obenchain vobencha at fhcrc.org
Mon Oct 7 17:55:29 CEST 2013

Hi Jose,

If the SummarizedExperiment objects have the same rowData you can use 
cbind() to combine the data into a single SE object. This combines the 
data in info() and assays() so the counts of each SE object end up in 
the assays()$counts matrix as separate columns.

cmb <- cbind(SE1, SE2)

In this way you can create one SE object that holds all counts for the 
different experiments. To sum the counts use rowSums() on the count matrix.



On 10/07/2013 05:43 AM, Garcia Manteiga Jose Manuel wrote:
> Dear Martin and BioC,
> I am using the Summarized Experiments object in DESeq2 to upload RNA-Seq data. I have resequenced a subset of samples in my experiment and re-counted them with htseq-count, therefore I end up with a subset of new files with new count data. I wondered whether there is a in-R way of using the SummarizedExperiments data object to sum up the counts of the second Run to the counts of the first run. Of course I know how to do without the DESeqDataSet and other DESeq functions but I thought that maybe there is a quick and safer way by using some `combine` onto 2 different dds (SE) objects of same rowData with samples to sum.
> Thanks in advance
> Best
> Jose
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