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DavisLaboratory / standR

Spatial transcriptomics analyses and decoding in R
https://davislaboratory.github.io/standR/
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Extract normalized expression matrix #12

Closed GeremyClair closed 1 year ago

GeremyClair commented 1 year ago

Hi there, I would like to retrieve the normalized expression as a simple data frame after performing the normalization in StandR can you guide me on how to do this. Thank you in advance for your help Geremy Clair

ningbioinfo commented 1 year ago

Hi Geremy,

Assuming you're doing normalization using spe <- geomxNorm(spe, method = "TMM") You can do df <- assay(spe, "logcounts") or df <- assay(spe, 2) to get the norm count table.

GeremyClair commented 1 year ago

Thank you for your answer, it is appreciated. I was able to figure from your code that you were using EdgeR for the normalization. I therefore performed the normalization outside of the spatial object, but this is good information for the next time around!