[BioC] Summarized Experiments - Combine

Garcia Manteiga Jose Manuel garciamanteiga.josemanuel at hsr.it
Tue Oct 8 12:46:39 CEST 2013

Thanks Valerie,
I have used  both techniques. First I have created an SE object with cbind that was the 'union' of both. Then I have changed the colums(samples) by using a rowSums command like yours on the SE.sum counts
I noticed that there is a `collapse` procedure in the Vignette of parathyroidSE for technical replicates that could be more or less the same.
Thank you all,

On Oct 7, 2013, at 5:55 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:

> 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()$counts matrix as separate columns.
> cmb <- cbind(SE1, SE2)
> In this way you can create one SE object that holds all counts for the 
> different experiments. To sum the counts use rowSums() on the count matrix.
> rowSums(assays(cmb)$counts)
> Valerie
> 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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