Merging multiple single cell experiment objects from different samples
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achoppe • 0
@375a1478
Last seen 26 days ago
Australia

Hello! I am analysing a large 10x scRNA-seq run. I made separate sce objects for each participant sample so I could inspect them on their own and perform initial QC, and now I want to merge just two of them into one sce object for normalisation and further analysis. I will eventually merge 12 sce objects together but want to see if it works with 2 objects first. I thought it would be a simple merge of the objects but I am getting this error: Error in DataFrame(..., check.names = FALSE) : different row counts implied by arguments

sce_all_data <- cbind(sce002,sce003)

Is this because I have different cell numbers in each sce object? After QC I have 19,989 cells in one sce and 19,943 in the other. Is there a way to get around this? Thank you for any advice you have!!

sessionInfo( ) R version 4.0.4 (2021-02-15) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] dendextend_1.15.2 pheatmap_1.0.12 forcats_0.5.1 purrr_0.3.4 readr_2.1.2
[6] tibble_3.1.6 tidyverse_1.3.1 tidyr_1.2.0 plyr_1.8.7 reshape2_1.4.4
[11] stringr_1.4.0 dplyr_1.0.8 plotly_4.10.0 data.table_1.14.2 readxl_1.4.0
[16] scRNAseq_2.4.0 uwot_0.1.11 Matrix_1.4-1 scater_1.18.6 ggplot2_3.3.5
[21] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 Biobase_2.50.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
[26] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.1 MatrixGenerics_1.2.1 matrixStats_0.62.0

sce SingleCellExperiment merge • 293 views
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You may have a look at sce_cbind function from the scMerge package (https://sydneybiox.github.io/scMerge/reference/sce_cbind.html) because the issue here is indeed that you have different number of rows, you might to select common rows manually or directly use sce_cbind function

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Thanks Basti! I am trying to get that to work - will reply later today if it does. Had trouble installing scMerge but finally got it to work by installing an earlier version of Hmisc.

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I think it worked! Merci Basti 🙏 I made a sce_list of the two sce objects, then used this code: sce_list <- list((sce002),(sce003)) sce<- sce_cbind( sce_list, method = "intersect", exprs = c("counts"), colData_names = NULL) I removed any of the arguments related to batch as these cells are from the same batch, just different participants. Does that look right to you? Are there any other arguments I should have added you think? There are many here: https://sydneybiox.github.io/scMerge/reference/scMerge.html Thanks again!

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Just in case this helps anyone else - you need to have the argument colData_names = TRUE to keep the metadata information for each sce object.

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