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verified publisher icon KrishnaswamyLab

Magic + seurat workflow

Open anemartinezlarrinaga2898 opened this issue 3 years ago • 4 comments

Hello!

I have found the paper and I think is pretty nice tool, but have some questions:

  1. Can It be applied with integrated data? The data has been integrated with Seurat and normalized with log.
  2. Which one will be the best normalization method? SCT or stay with the log normalization.
  3. Also does anyone perform downstream analysis with the default assay being the MAGIC output? Such as ligan receptor analysis

Thank you in advanced!

anemartinezlarrinaga2898 avatar Sep 20 '22 10:09 anemartinezlarrinaga2898

Wow, we have the same questions and applications. Did you solve it?

LucaTucciarone avatar Nov 01 '22 20:11 LucaTucciarone

Nop, I decided to look for other tools where I have more info on how to work with them!

Sorry

anemartinezlarrinaga2898 avatar Nov 02 '22 11:11 anemartinezlarrinaga2898

Could u share what tools you landed on in the end? I tried their normalization but I get a ton of NaNs, I am running using SCT now, I shall see what happens but I am open to other tools

LucaTucciarone avatar Nov 02 '22 18:11 LucaTucciarone

With Magic I manage to run it but in Python, couldn't manage to do it in R. Also I dint like that the parameter selection is so biased to the user.

Im going to use SAVER https://www.nature.com/articles/s41592-018-0033-z it does benchmark with Magic and it seems more robust and less biased.

Hope it helps!

anemartinezlarrinaga2898 avatar Nov 03 '22 11:11 anemartinezlarrinaga2898