Error: se does not inherit from class SummarizedExperiment
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Wuschel ▴ 10
@wuschel-15944
Last seen 22 months ago
HUJI

Hi,

I am using DEP package for analysis of deferentially enriched proteins. I get an error when testing comparisions, this same scripts worked in my old PC.

data_diff_manual <- test_diff(data_imp_knn, type = "manual", 
+                               test = c('mut_0h__vs_WT_0h_', 
+                                        'mut_0h__vs_WT_0h_',
+                                        'mut_0h__vs_WT_0h_'))

Error message:

Error: se does not inherit from class SummarizedExperiment

How can I fix this?
DEP SummarizedExperiment • 2.4k views
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Hi Wuschel,

Please provide more information, so that I have a working example of the error. The error states that one of your input objects that should be of the class SummarizedExperiment, which is the object class that the DEP package is working with, is not a SummarizedExperiment.

Best, Arne

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deleted entry: double entry

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Hi Arne,

This is my R details;

> version
               _                           
platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          3                           
minor          6.1                         
year           2019                        
month          07                          
day            05                          
svn rev        76782                       
language       R                           
version.string R version 3.6.1 (2019-07-05)
nickname       Action of the Toes

This is Package details details:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

other attached packages:
 [1] imputeLCMD_2.0              impute_1.58.0               pcaMethods_1.76.0          
 [4] norm_1.0-9.5                tmvtnorm_1.4-10             gmm_1.6-2                  
 [7] sandwich_2.5-1              Matrix_1.2-17               mvtnorm_1.0-11             
[10] SummarizedExperiment_1.14.0 DelayedArray_0.10.0         BiocParallel_1.17.18       
[13] matrixStats_0.54.0          Biobase_2.44.0              GenomicRanges_1.36.0       
[16] GenomeInfoDb_1.20.0         IRanges_2.18.1              S4Vectors_0.22.0           
[19] BiocGenerics_0.30.0         fitdistrplus_1.0-14         npsurv_0.4-0               
[22] lsei_1.2-0                  survival_2.44-1.1           MASS_7.3-51.4              
[25] DEP_1.6.0                   data.table_1.12.2           forcats_0.4.0              
[28] stringr_1.4.0               dplyr_0.8.3                 purrr_0.3.2                
[31] readr_1.3.1                 tidyr_0.8.3                 tibble_2.1.3               
[34] ggplot2_3.2.0               tidyverse_1.2.1            

loaded via a namespace (and not attached):
 [1] colorspace_1.4-1       rjson_0.2.20           circlize_0.4.6        
 [4] XVector_0.24.0         GlobalOptions_0.1.0    clue_0.3-57           
 [7] rstudioapi_0.10        mzR_2.18.0             affyio_1.54.0         
[10] ggrepel_0.8.1          DT_0.7                 lubridate_1.7.4       
[13] xml2_1.2.1             splines_3.6.1          codetools_0.2-16      
[16] ncdf4_1.16.1           doParallel_1.0.14      zeallot_0.1.0         
[19] jsonlite_1.6           broom_0.5.2            cluster_2.1.0         
[22] vsn_3.52.0             png_0.1-7              shinydashboard_0.7.1  
[25] shiny_1.3.2            BiocManager_1.30.4     compiler_3.6.1        
[28] httr_1.4.0             backports_1.1.4        assertthat_0.2.1      
[31] lazyeval_0.2.2         limma_3.40.6           cli_1.1.0             
[34] later_0.8.0            htmltools_0.3.6        tools_3.6.1           
[37] gtable_0.3.0           glue_1.3.1             GenomeInfoDbData_1.2.1
[40] affy_1.62.0            Rcpp_1.0.2             MALDIquant_1.19.3     
[43] cellranger_1.1.0       vctrs_0.2.0            preprocessCore_1.46.0 
[46] nlme_3.1-140           iterators_1.0.12       rvest_0.3.4           
[49] mime_0.7               XML_3.98-1.20          zlibbioc_1.30.0       
[52] zoo_1.8-6              scales_1.0.0           MSnbase_2.10.1        
[55] hms_0.5.0              promises_1.0.1         ProtGenerics_1.16.0   
[58] RColorBrewer_1.1-2     ComplexHeatmap_2.0.0   yaml_2.2.0            
[61] gridExtra_2.3          stringi_1.4.3          foreach_1.4.7         
[64] shape_1.4.4            rlang_0.4.0            pkgconfig_2.0.2       
[67] bitops_1.0-6           mzID_1.22.0            lattice_0.20-38       
[70] labeling_0.3           htmlwidgets_1.3        tidyselect_0.2.5      
[73] plyr_1.8.4             magrittr_1.5           R6_2.4.0              
[76] generics_0.0.2         pillar_1.4.2           haven_2.1.1           
[79] withr_2.1.2            RCurl_1.95-4.12        modelr_0.1.4          
[82] crayon_1.3.4           fdrtool_1.2.15         GetoptLong_0.1.7      
[85] grid_3.6.1             readxl_1.3.1           digest_0.6.20         
[88] xtable_1.8-4           httpuv_1.5.1           munsell_0.5.0         
>
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DEP Steps;

# Impute missing data using the k-nearest neighbour approach (for MAR)
data_imp_knn <- impute(data_filt, fun = "knn", rowmax = 0.9)

    data_diff_manual <- test_diff(data_imp_knn, type = "manual", 
    +                               test = c('mut_0h__vs_WT_0h_', 
    +                                        'mut_0h__vs_WT_0h_',
    +                                        'mut_0h__vs_WT_0h_'))

Error Message:

   Error: se does not inherit from class SummarizedExperiment
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* installing *source* package 'DEP' ...
** using staged installation
** R
Warning: no function found corresponding to methods exports from 'GenomicRanges' for: 'FactorToClass'
Warning: no function found corresponding to methods exports from 'DelayedArray' for: 'splitAsList'
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'ProtGenerics' 1.16.0 is already loaded, but >= 1.17.2 is required
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'DEP'
* removing 'C:/Users/AWY/Documents/R/win-library/3.6/DEP'
Warning in install.packages :
  installation of package ‘C:/Users/AWY/Desktop/DEP_1.7.0.tar.gz’ had non-zero exit status
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1
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For installation problems, be sure that you are in a new R session with no other R sessions running. Use the command BiocManager::valid() to check that you have a consistent installation.

It looks like you're trying to use a 'devel' version of DEP (the odd number, '.7' in the version) and you're trying to install from source. Instead, either install the current release version BiocManager::install("DEP") or upgrade your entire installation to 'devel' BiocManager::install(version="devel") and then install the devel version of DEP BiocManager::install("DEP").

I do not have any experience with DEP, but installing inconsistent versions of packages is likely to result in the types of errors you are reporting.

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Hi Martin, Thank you for helping with this. This is my session info after reinstalling everything. Unfortunately Still I get this "Error: se does not inherit from class SummarizedExperiment "

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

other attached packages:
 [1] imputeLCMD_2.0              impute_1.58.0               pcaMethods_1.76.0          
 [4] norm_1.0-9.5                tmvtnorm_1.4-10             gmm_1.6-2                  
 [7] sandwich_2.5-1              Matrix_1.2-17               mvtnorm_1.0-11             
[10] SummarizedExperiment_1.14.1 DelayedArray_0.10.0         BiocParallel_1.17.18       
[13] matrixStats_0.54.0          Biobase_2.44.0              GenomicRanges_1.36.0       
[16] GenomeInfoDb_1.20.0         IRanges_2.18.1              S4Vectors_0.22.0           
[19] BiocGenerics_0.30.0         fitdistrplus_1.0-14         npsurv_0.4-0               
[22] lsei_1.2-0                  survival_2.44-1.1           MASS_7.3-51.4              
[25] DEP_1.6.0                   data.table_1.12.2           forcats_0.4.0              
[28] stringr_1.4.0               dplyr_0.8.3                 purrr_0.3.2                
[31] readr_1.3.1                 tidyr_0.8.3                 tibble_2.1.3               
[34] ggplot2_3.2.0               tidyverse_1.2.1            

loaded via a namespace (and not attached):
 [1] colorspace_1.4-1       rjson_0.2.20           circlize_0.4.6         XVector_0.24.0        
 [5] GlobalOptions_0.1.0    clue_0.3-57            rstudioapi_0.10        mzR_2.18.0            
 [9] affyio_1.54.0          DT_0.7                 lubridate_1.7.4        xml2_1.2.1            
[13] splines_3.6.1          codetools_0.2-16       ncdf4_1.16.1           doParallel_1.0.15     
[17] zeallot_0.1.0          jsonlite_1.6           broom_0.5.2            cluster_2.1.0         
[21] vsn_3.52.0             png_0.1-7              shinydashboard_0.7.1   shiny_1.3.2           
[25] BiocManager_1.30.4     compiler_3.6.1         httr_1.4.0             backports_1.1.4       
[29] assertthat_0.2.1       lazyeval_0.2.2         limma_3.40.6           cli_1.1.0             
[33] later_0.8.0            htmltools_0.3.6        tools_3.6.1            gtable_0.3.0          
[37] glue_1.3.1             GenomeInfoDbData_1.2.1 affy_1.62.0            Rcpp_1.0.2            
[41] MALDIquant_1.19.3      cellranger_1.1.0       vctrs_0.2.0            preprocessCore_1.46.0 
[45] nlme_3.1-140           iterators_1.0.12       rvest_0.3.4            mime_0.7              
[49] XML_3.98-1.20          zlibbioc_1.30.0        zoo_1.8-6              scales_1.0.0          
[53] MSnbase_2.10.1         hms_0.5.0              promises_1.0.1         ProtGenerics_1.16.0   
[57] RColorBrewer_1.1-2     ComplexHeatmap_2.0.0   yaml_2.2.0             gridExtra_2.3         
[61] stringi_1.4.3          foreach_1.4.7          shape_1.4.4            rlang_0.4.0           
[65] pkgconfig_2.0.2        bitops_1.0-6           mzID_1.22.0            lattice_0.20-38       
[69] labeling_0.3           htmlwidgets_1.3        tidyselect_0.2.5       plyr_1.8.4            
[73] magrittr_1.5           R6_2.4.0               generics_0.0.2         pillar_1.4.2          
[77] haven_2.1.1            withr_2.1.2            RCurl_1.95-4.12        modelr_0.1.4          
[81] crayon_1.3.4           GetoptLong_0.1.7       grid_3.6.1             readxl_1.3.1          
[85] digest_0.6.20          xtable_1.8-4           httpuv_1.5.1           munsell_0.5.0
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0
Entering edit mode

From the documentation ?test_diff and Arne's answer, it seems like your object data_imp_knn should be a SummarizedExperiment, i.e., is(data_imp_knn, "SummarizedExperiment") should return TRUE. Does it?

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