Question: BASiCS spike info for single cell RNA sequences or Bayesian statistics help
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gravatar for alexandriapinto1
14 months ago by
alexandriapinto110 wrote:

Hi, 

I am dealing with a dataset and I do not believe any spike in were included. I want to use BASiCS to help my clustering but it requires the use of spike information. Is there a way to use BASiCs without the information?

Alternatively, is there another package I could use to use bayesian statistics on my data? 

 

 

ADD COMMENTlink modified 14 months ago by CataVallejos10 • written 14 months ago by alexandriapinto110
Answer: BASiCS spike info for single cell RNA sequences or Bayesian statistics help
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gravatar for CataVallejos
14 months ago by
CataVallejos10
The Alan Turing Institute
CataVallejos10 wrote:

Hello,

Indeed, the current release of BASiCS (BioC 3.6) cannot be used without spike-ins. Recently, we extended the method to the no-spikes case and that is available in BioC devel (see also https://www.biorxiv.org/content/early/2017/12/21/237214)

 

However, I am afraid that BASiCS is *not* suitable for clustering analyses. This is because BASiCS has been designed in the context of supervised experimental designs only (e.g. case/control). Applying BASiCS in a clustering context is not advised and therefore I would refer you to other libraries that are specifically designed for clustering (e.g. SC3). 

My apologies for not being more helpful this time.

Best

Cata

 

 

ADD COMMENTlink written 14 months ago by CataVallejos10

Ah okay! Thank you anyway

ADD REPLYlink written 14 months ago by alexandriapinto110
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