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feiyoung / PRECAST

an efficient data integration method for multiple spatial transcriptomics data with non- cluster-relevant effects such as the complex batch effects.
GNU General Public License v3.0
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PRECAST IntegrateSpaData errors #2

Closed anvaly closed 1 year ago

anvaly commented 1 year ago

Hello, when I try to run the package I encounter the following two errors:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': Cannot find 'RNA' in this Seurat object

This stems from line 9 of IntegrateSpaData: XList <- lapply(PRECASTObj@seulist, function(x) Matrix::t(x[["RNA"]]@data))

Is the intention of this line to use the normalized or non-normalized assay of the Seurat object? (E.g., Spatial or SCT)

If I fix this error by copying one of the existing assays (Spatial or SCT) to an assay named "RNA", I experience another error.

Error in intersect((genelist), Mouse_HK_genes$Gene) : object 'Mouse_HK_genes' not found

This stems from line 24 of IntegrateSpaData: houseKeep <- switch(lower_species, human = { intersect((genelist), Mouse_HK_genes$Gene)

The script is trying to reach for the mouse gene list that wasn't defined. What is the exact purpose of this list?

feiyoung commented 1 year ago

Thank you for feedback. Yes, this intention of that line is to use the normalized assay.

We have updated the function IntegrateSpaData() in new version 1.5 of PRECAST. You can re-install PRECAST from github by commond: remotes::install_github("feiyoung/PRECAST").

Before using PRECAST, please read our tutorial https://feiyoung.github.io/PRECAST/articles/PRECAST.BreastCancer.html; then try again. To avoid error, one user can strictly follow the step given in the tutorial.

anvaly commented 1 year ago

Thank you for your response! Indeed, upgrading from 1.4 to 1.5 fixed these two issues.