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BodenmillerGroup / IMCDataAnalysis

R based workflow for multiplexed imaging data
https://bodenmillergroup.github.io/IMCDataAnalysis/
MIT License
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Normalize is defunct #82

Closed tryggest closed 1 year ago

tryggest commented 1 year ago

I am trying to run the script in R. Following the guide I have read in the data as per section 7. But when I proceed from there I get an error message:

> cur_images <- cytomapper::normalize(cur_images, separateImages = TRUE)

Error: 'normalize' is defunct. Use ''normalize,SingleCellExperiment-method' is defunct. Use 'logNormCounts' instead' instead. See help("Defunct")

Is there a way around this?

tryggest commented 1 year ago

Found a typo in my own code. Sorry.

Closing issue