MultiCondData example dataset?

[byee4]

Is there an example MultiCondData? I am trying to follow the vignette example for multiple conditions, but am running into an unknown error:

R 

R version 3.4.1 (2017-06-30) -- "Single Candle"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library('SCnorm')
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

Matrix products: default
BLAS: /projects/ps-yeolab/software/eclipconda/envs/scnorm-0.99.5/lib/R/lib/libRblas.so
LAPACK: /projects/ps-yeolab/software/eclipconda/envs/scnorm-0.99.5/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C                  
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915    
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915   
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C                     
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C                
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C           

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

other attached packages:
[1] SCnorm_0.99.5

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               cluster_2.0.6             
 [3] XVector_0.16.0             GenomicRanges_1.28.4      
 [5] BiocGenerics_0.22.0        zlibbioc_1.22.0           
 [7] IRanges_2.10.2             munsell_0.4.3             
 [9] BiocParallel_1.10.1        lattice_0.20-35           
[11] colorspace_1.3-2           rlang_0.1.2               
[13] plyr_1.8.4                 GenomeInfoDb_1.12.2       
[15] tools_3.4.1                SummarizedExperiment_1.6.3
[17] parallel_3.4.1             grid_3.4.1                
[19] data.table_1.10.4          Biobase_2.36.2            
[21] gtable_0.2.0               quantreg_5.33             
[23] MatrixModels_0.4-1         matrixStats_0.52.2        
[25] lazyeval_0.2.0             tibble_1.3.4              
[27] Matrix_1.2-11              GenomeInfoDbData_0.99.0   
[29] ggplot2_2.2.1              S4Vectors_0.14.3          
[31] bitops_1.0-6               RCurl_1.95-4.8            
[33] DelayedArray_0.2.7         compiler_3.4.1            
[35] moments_0.14               scales_0.5.0              
[37] stats4_3.4.1               SparseM_1.77              
> data(ExampleSimSCData)
> ExampleSimSCData[1:5,1:5]
          Cell_1     Cell_2    Cell_3    Cell_4    Cell_5
Gene_1  3.809447  0.5891684  6.505612 33.052416  0.000000
Gene_2 21.703998  3.9118515  0.000000  0.000000  5.651665
Gene_3  2.128070  0.0000000 11.587132 11.352172  5.402953
Gene_4 22.681505  0.0000000 27.495737  2.571482  8.248906
Gene_5  0.000000 23.9983434 38.810055  1.244605 12.693561
> dim(ExampleSimSCData)       
[1] 5000   90
> Conditions = rep(c(1, 2), each= 45)
> DataNorm <- SCnorm(Data = ExampleSimSCData, Conditions = Conditions)
Setting up parallel computation using 15 cores
Gene filter is applied within each condition.
Error in names(GeneFilterOUT) <- paste0("GenesFilteredOutGroup", unique(Conditions)) : 
  'names' attribute [2] must be the same length as the vector [1]
In addition: Warning messages:
1: In seq_len(Levels) : first element used of 'length.out' argument
2: In seq_len(Levels) : first element used of 'length.out' argument
3: In seq_len(Levels) : first element used of 'length.out' argument
4: In seq_len(Levels) : first element used of 'length.out' argument
5: In seq_len(Levels) : first element used of 'length.out' argument
6: In seq_len(Levels) : first element used of 'length.out' argument
7: In seq_len(Levels) : first element used of 'length.out' argument
8: In seq_len(Levels) : first element used of 'length.out' argument

[rhondabacher]

Hi Brian,

Thanks for using SCnorm. It looks like you're using an older version of SCnorm (likely the error is a bug I accidently created while recoding for Bioconductor submission). I apologize for any inconvenience. Everything should work fine if you download from Bioconductor at: https://bioconductor.org/packages/devel/bioc/html/SCnorm.html

or just redownloading via Github: library(devtools) devtools::install_github("rhondabacher/SCnorm")

Please let me know if you encounter any further errors.

Best, Rhonda

[byee4]

yup that seemed to work, thank you!