Hello,
I am trying to use Startrac.run() with two different sample types: PBMC and Tissue.
Each dataset was annotated separately, meaning that the cluster annotations differ between PBMC and Tissue.
When I run Startrac.run(), I get the following error during the pairwise index calculation:
Error in dcast(cls.migr.index.df, majorCluster ~ crossLoc, value.var = "pIndex.migr") :
The dcast generic in data.table has been passed a data.frame, but data.table::dcast currently only has a method for data.tables.
Please confirm your input is a data.table, with setDT(cls.migr.index.df) or as.data.table(cls.migr.index.df).
If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is superseded and is no longer actively developed.
Question
Is Startrac.run() designed to work only when PBMC and Tissue share the same annotation scheme?
If PBMC and Tissue have different cluster annotations, is it still possible to use Startrac.run() for analysis?
What would be the best approach to handle this situation? Should I manually match the cluster names before running Startrac?
I appreciate any guidance on how to properly use Startrac in this case.
Thank you! 😊
Hello,
I am trying to use Startrac.run() with two different sample types: PBMC and Tissue.
Each dataset was annotated separately, meaning that the cluster annotations differ between PBMC and Tissue.
When I run Startrac.run(), I get the following error during the pairwise index calculation:
Error in dcast(cls.migr.index.df, majorCluster ~ crossLoc, value.var = "pIndex.migr") :
The dcast generic in data.table has been passed a data.frame, but data.table::dcast currently only has a method for data.tables.
Please confirm your input is a data.table, with setDT(cls.migr.index.df) or as.data.table(cls.migr.index.df).
If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is superseded and is no longer actively developed.
Question
Is Startrac.run() designed to work only when PBMC and Tissue share the same annotation scheme?
If PBMC and Tissue have different cluster annotations, is it still possible to use Startrac.run() for analysis?
What would be the best approach to handle this situation? Should I manually match the cluster names before running Startrac?
I appreciate any guidance on how to properly use Startrac in this case.
Thank you! 😊