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How to scale data matrix in Seurat

I am trying to scale a single-cell data matrix in Seurat and I am not being able because of the GB it occupies. I am trying to find an alternative way to do it because I am analysing integrated datasets and I do not know if it makes sense to scale data in differentes parts (for example: use SplitObject in seurat to split data and scale them individually).

scale
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updated by marco.barr • marco.barr • written by frarodmar17 • frarodmar17

Seurat’s documentation explains what to do for jobs and data that require a lot of memory at this link: https://satijalab.org/seurat/archive/v3.0/future_vignette.html.
Check the number of cores your machine has with availableCores(). For example in my script I added these lines upstream of the analysis:

plan(cluster, workers = 8)
options(future.globals.maxSize = 8000 * 1024 2, 
        future.rng.onMisuse = "ignore")

You can adapt it to your needs. In these cases I recommend to run the scripts on a HPC system

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written by marco.barr • marco.barr

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