Entering edit mode
Hello,
I got an error when running the software.
I just followed the:
https://www.biostat.wisc.edu/~kendzior/SCNORM/SCnorm_vignette.pdf
Thank you in advance for your great help!
Best,
Yue
> DataNorm <- SCnorm(Data = MultiCondData,
+ Conditions = Conditions,
+ PrintProgressPlots = TRUE,
+ FilterCellNum = 10,
+ NCores=3,
+ useZerosToScale=TRUE)
Error in methods::is(Data, "SummarizedExperiment") :
object 'MultiCondData' not found
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SCnorm_1.8.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 plyr_1.8.5
[3] compiler_3.6.1 pillar_1.4.3
[5] BiocManager_1.30.10 GenomeInfoDb_1.22.0
[7] XVector_0.26.0 moments_0.14
[9] bitops_1.0-6 tools_3.6.1
[11] zlibbioc_1.32.0 digest_0.6.25
[13] SingleCellExperiment_1.8.0 lifecycle_0.1.0
[15] tibble_2.1.3 gtable_0.3.0
[17] lattice_0.20-40 pkgconfig_2.0.3
[19] rlang_0.4.4 Matrix_1.2-17
[21] DelayedArray_0.12.2 parallel_3.6.1
[23] SparseM_1.78 GenomeInfoDbData_1.2.2
[25] stringr_1.4.0 cluster_2.1.0
[27] dplyr_0.8.4 MatrixModels_0.4-1
[29] S4Vectors_0.24.3 IRanges_2.20.2
[31] tidyselect_1.0.0 stats4_3.6.1
[33] grid_3.6.1 data.table_1.12.8
[35] glue_1.3.1 Biobase_2.46.0
[37] R6_2.4.1 BiocParallel_1.20.1
[39] farver_2.0.3 reshape2_1.4.3
[41] purrr_0.3.3 magrittr_1.5
[43] ggplot2_3.2.1 scales_1.1.0
[45] matrixStats_0.55.0 BiocGenerics_0.32.0
[47] GenomicRanges_1.38.0 assertthat_0.2.1
[49] SummarizedExperiment_1.16.1 colorspace_1.4-1
[51] labeling_0.3 quantreg_5.54
[53] stringi_1.4.6 RCurl_1.98-1.1
[55] lazyeval_0.2.2 munsell_0.5.0
[57] crayon_1.3.4
This is somewhat expected. The maintainers showed runnable code up to this point and are just displaying the possible function call when you have a dataset with
Multiple Conditions. It demonstrates other arguments to the main function call that could be of use. In order for the function to run, you would need to define MultiCondData and appropriate Conditions where multiple conditions are present.shepherl's response is exactly right. I will make this clearer in the vignette as well. If you're interested in running an example, you could arbitrarily define the example dataset "ExampleSimSCData" of 90 cells to have two conditions with 45 cells each and do:
Conditions = rep(c(1, 2), each= 45) MultiCondData = ExampleSimSCData DataNorm <- SCnorm(Data = ​MultiCondData, Conditions = Conditions, PrintProgressPlots = TRUE FilterCellNum = 10, NCores=3, useZerosToScale=TRUE)
Hello, rbacher,
Thank you so much for your great help!
These codes works!
Thank you again!
Best!
Yue
Hello, shepherl,
Thank you so much for your great help!
Best,
Yue