Hello,

Thanks for developing so nice R package SCnorm.

I just followed the manual. I got this error at the last paragraph in the section 3 SCnorm: Multiple Conditions when running the function scaleNormMultCont.

Thank you in advance for great help!

Best,

Yue

> normalizedDataSet1 <- results(DataNorm1, type = "NormalizedData")
> normalizedDataSet2 <- results(DataNorm2, type = "NormalizedData")
> NormList <- list(list(NormData = normalizedDataSet1), list(NormData = normalizedDataSet2))
> OrigData <- ExampleSimSCData
> Genes <- rownames(ExampleSimSCData)
> useSpikes = FALSE
> useZerosToScale = FALSE
> DataNorm <- scaleNormMultCont(NormData = NormList,
+ OrigData = OrigData,
+ Genes = Genes, useSpikes = useSpikes,
+ useZerosToScale = useZerosToScale)
 Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘counts’ for signature ‘"matrix"’


> 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