different between SCTransform and NormalizeData
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17 months ago
re_raz ▴ 20

Hi Is there different between using SCTransform for single cell RNA-seq analysis or using NormalizeData? Is the result same? when I should use SCTransform or NormalizeData?

Thanks

R scRNA-seq Normalization SCTransform • 4.9k views
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17 months ago
ATpoint 57k

re_raz, please read available online documentation, papers and vignettes first before posting. The same goes for this question: differential expression from sc RNA seq

Yes, there is a difference, clearly outlined in the SCtransform paper. Results are not the same, please read the paper and the SCtransform vignette.

https://github.com/ChristophH/sctransform

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1874-1

https://satijalab.org/seurat/v3.0/sctransform_vignette.html

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I am new to bioinformatic and new user in biostars. I apologise

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No problem at all, we all were new at some point. By experience I can tell you that extensive reading is always beneficial of you are getting started with a new type of analysis since many of the common obstacles are described in the manuals/vignettes. If you then have specific questions feel free to post but please be sure to read the available resources first.

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Thanks for your advice

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