error in SCnorm
0
0
Entering edit mode
yueli7 ▴ 20
@yueli7-8401
Last seen 2.8 years ago
China

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
scnorm • 804 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

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)

ADD REPLY
0
Entering edit mode

Hello, rbacher,

Thank you so much for your great help!

These codes works!

Thank you again!

Best!

Yue

ADD REPLY
0
Entering edit mode

Hello, shepherl,

Thank you so much for your great help!

Best,

Yue

ADD REPLY

Login before adding your answer.

Traffic: 960 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6