Hello everyone,
currently, I'm trying to run a differential gene expression analysis on an RNA-Seq data set using R and the DESeq2 package.
However, there are several technical replicates in the count table. There is this function "collapseReplicates()" which allows me to collapse these.
For me, however, it's unclear if one could simply add these counts so that we have for this one patient not twice 4000 counts but then 8000, for instance. For other patients, for which are no technical replicates, however, the counts stay much lower. So shouldn't there be normalization? Or is this not mattering ?
Would be great if you can help me. :)
I think you ca go ahead and use the collapseReplicates() function to add those technical replicates and DESeq2 normalization takes care of those reads later on.
I, personally, wouldn't collapse them. If I understood your question correctly, you have technical replicates, right? I use EdgeR and provide it a design table where I indicate that the samples come from the same patient.
Natasha Jorge thanks for the info. How do you indicate that the samples come from the same patient in EdgeR?
Thank you!
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