zhengli09
commented
1 year ago Hi, It looks like this is an error caused by the Harmony package for batch effect removal. Do you mind sharing your BASS object information by printing your BASS object (print(BASS))? I am wondering if this is due to some data matching issue across slices. For each gene expression data, rows are genes and columns are cells, and the rows of the location matrix need to match the columns of the gene expression matrix.
Best, Zheng
Hello! I used BASS to integrate spatial transcriptome data of multi slices. I encounter an error using BASS.preprocess function.
Here is my session info:
[1] mclust_6.0.0 ggrepel_0.9.1
[3] Rcpp_1.0.8 rsvd_1.0.5
[5] lattice_0.20-45 foreach_1.5.2
[7] assertthat_0.2.1 SingleCellExperiment_1.18.1
[9] utf8_1.2.2 R6_2.5.1
[11] GenomeInfoDb_1.32.4 stats4_4.2.1
[13] pracma_2.4.2 pillar_1.8.1
[15] sparseMatrixStats_1.8.0 zlibbioc_1.42.0
[17] rlang_1.0.6 irlba_2.3.5.1
[19] S4Vectors_0.34.0 Matrix_1.5-1
[21] BiocNeighbors_1.14.0 BiocParallel_1.30.4
[23] RCurl_1.98-1.9 munsell_0.5.0
[25] beachmat_2.12.0 DelayedArray_0.22.0
[27] compiler_4.2.1 vipor_0.4.5
[29] BiocSingular_1.12.0 SPARK_1.1.1
[31] pkgconfig_2.0.3 BiocGenerics_0.42.0
[33] ggbeeswarm_0.6.0 tidyselect_1.2.0
[35] SummarizedExperiment_1.26.1 gridExtra_2.3
[37] tibble_3.1.8 GenomeInfoDbData_1.2.8
[39] IRanges_2.30.1 codetools_0.2-18
[41] matrixStats_0.62.0 viridisLite_0.4.1
[43] fansi_1.0.3 dplyr_1.0.10
[45] withr_2.5.0 bitops_1.0-7
[47] grid_4.2.1 gtable_0.3.1
[49] lifecycle_1.0.3 DBI_1.1.3
[51] magrittr_2.0.3 scales_1.2.1
[53] ScaledMatrix_1.4.1 cli_3.4.1
[55] stringi_1.7.8 scuttle_1.6.3
[57] XVector_0.36.0 viridis_0.6.2
[59] doParallel_1.0.17 scater_1.24.0
[61] DelayedMatrixStats_1.18.2 generics_0.1.3
[63] vctrs_0.5.0 iterators_1.0.14
[65] tools_4.2.1 harmony_0.1.1
[67] CompQuadForm_1.4.3 Biobase_2.56.0
[69] glue_1.6.2 beeswarm_0.4.0
[71] MatrixGenerics_1.8.1 parallel_4.2.1
[73] colorspace_2.0-3 GenomicRanges_1.48.0
[75] matlab_1.0.4