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rargelaguet / scnmt_gastrulation

scNMT-seq gastrulation
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unable to find an inherited method for function ‘exprs’ for signature ‘"SingleCellExperiment"’ #2

Closed Van1yu3 closed 4 years ago

Van1yu3 commented 4 years ago

Hi!

When I tried reproducing your result on the MOFA method, I got an error which I failed to deal with.

More specifically, I failed to use exprs() function on the SingleCellExperiment class, and got the following error message when I ran the code here:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘exprs’ for signature ‘"SingleCellExperiment"’

My sessionInfo() is as follows:

R version 3.5.3 (2019-03-11) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /home/user/software/R-353/lib64/R/lib/libRblas.so LAPACK: /home/user/software/R-353/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] SingleCellExperiment_1.4.1 SummarizedExperiment_1.12.0 [3] DelayedArray_0.8.0 BiocParallel_1.16.6 [5] matrixStats_0.56.0 Biobase_2.42.0 [7] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 [9] IRanges_2.16.0 S4Vectors_0.20.1 [11] BiocGenerics_0.28.0 purrr_0.3.3 [13] data.table_1.12.8

loaded via a namespace (and not attached): [1] lattice_0.20-38 bitops_1.0-6 grid_3.5.3 [4] magrittr_1.5 zlibbioc_1.28.0 rlang_0.4.5 [7] XVector_0.22.0 Matrix_1.2-15 tools_3.5.3 [10] RCurl_1.98-1.1 compiler_3.5.3 GenomeInfoDbData_1.2.0

I wonder if it's my own problem?

Thanks a lot!

rargelaguet commented 4 years ago

Hi, I think is because of an update in SingleCellExperiment where expr(sce) has been replaced by logcounts(sce). Can you check?

Van1yu3 commented 4 years ago

When I replaced exprs by logcounts, the error no more occurred. However, I did not see any updating message about this exprs function on either the reference manual or the news in this SingleCellExperiment package. May I ask how you know about that?

rargelaguet commented 4 years ago

The reason I found out is the same as you :) After updating the packages, expr(sce) stopped working and when checking the last vignettes I noticed they used logcounts(sce) instead. I will update the scripts in the repository. Thanks for reporting!

Van1yu3 commented 4 years ago

Thanks a lot for your instant reply! Then this issue can be closed.