Edward Zhao

Not super sure without knowing more about what SpotClean does. Most likely issue is the ordering of spots. Can you make sure the barcode order (column names) are the same...

Do you have just 1 Seurat object or multiple?

` install.packages("devtools") devtools::install_github("immunogenomics/harmony") ` can you try installing from github and retrying?

It seems like they require character vector input now for the grouping variable. Try adding this: ```r sce.combined$sample_name = as.character(sce.combined$sample_name) ```

Sorry I wasn't able to respond sooner. Selecting # of clusters is in general a pretty hard problem in clustering. I think the gap statistic could work in theory but...

Hi Dario, BayesSpace uses both the array and pixel coordinates to find neighbors. Array coordinates go to row/col and pixel coordinages go to imagerow/imagecol.

See the SCE and SummarizedExperiment manual pages for info on how to create the object: https://rdrr.io/bioc/SingleCellExperiment/man/SingleCellExperiment.html https://www.rdocumentation.org/packages/SummarizedExperiment/versions/1.2.3/topics/RangedSummarizedExperiment-class You can add the count matrix (genes * spots) to the counts slot...

In c++, % is the element-wise matrix multiplication operator, while * is for regular matrix multiplication.

There are 2 parameterizations of the gamma distribution: https://en.wikipedia.org/wiki/Gamma_distribution In Bayesian statistics, we typically use $\alpha$ and $\beta$, but the R function we used had the other parameterization, where $\theta...

your simulated PCA matrix has a singular covariance matrix. probably need to change up your data generating steps to make it more realistic. side note, BayesSpace isn't finding neighbors on...