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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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Error in ICM.EM(XList, q, K, AdjList = AdjList, beta_grid = beta_grid, : ncols of XList's components must be the same! #19

Open 1667857557 opened 9 months ago

1667857557 commented 9 months ago

Hi, Thank you for this great work! We encountered a problem when using the dataset from https://datadryad.org/stash/dataset/doi:10.5061/dryad.h70rxwdmj, we tried to combine 17 different GBM samples, however, the software reports the error:

> PRECASTObj <- PRECAST(PRECASTObj, K = 16)
Error in ICM.EM(XList, q, K, AdjList = AdjList, beta_grid = beta_grid,  : 
  ncols of XList's components must be the same!

Here is our code, can you give me some advice? I appreciate any help you can provide.

preobj <- CreatePRECASTObject(seuList = bc2, project = "GBM", selectGenesMethod = "HVGs", gene.number = 2000)
PRECASTObj <- AddAdjList(PRECASTObj, platform = "Visium")
PRECASTObj <- AddParSetting(PRECASTObj, Sigma_equal = FALSE, verbose = TRUE, maxIter = 30)
PRECASTObj <- PRECAST(PRECASTObj, K = 16)

Huang

feiyoung commented 9 months ago

You could try: PRECASTObj <- CreatePRECASTObject(seuList = bc2, project = "GBM", selectGenesMethod = "HVGs", gene.number = 2000) PRECASTObj <- AddAdjList(PRECASTObj, platform = "Visium")