se does not inherit from class SummarizedExperiment

Question

[yueli7]

Hello,

I used DEP on SILAC protein data.

Thank you in advance for your great help!

Best,

Yue

> SummarizedExperiment(assays=list(counts=counts_LH),
+                      rowRanges=rowRanges_LH, colData=colData_LH)
class: RangedSummarizedExperiment 
dim: 6674 12 
metadata(0):
assays(1): counts
rownames(6674): 4501853 4501857 ... 386643034 386643035
rowData names(1): feature_id
colnames(12): A B ... K L
colData names(1): Treatment

> plot_frequency(SummarizedExperiment)
Error: se does not inherit from class SummarizedExperiment



> 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               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] shinydashboard_0.7.1        tibble_3.0.4                shiny_1.5.0                 DEP_1.8.0                  
 [5] dplyr_1.0.2                 SummarizedExperiment_1.16.1 DelayedArray_0.12.3            BiocParallel_1.20.1        
 [9] matrixStats_0.57.0          Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
[13] IRanges_2.20.2              S4Vectors_0.24.4            BiocGenerics_0.32.0         ggplot2_3.3.2              
[17] proteus_0.2.14              proteusSILAC_0.1.0          limma_3.42.2               

loaded via a namespace (and not attached):
[1] backports_1.2.0        circlize_0.4.11        Hmisc_4.4-1            plyr_1.8.6            
[5] gmm_1.6-5              splines_3.6.1          crosstalk_1.1.0.1      digest_0.6.27         
[9] foreach_1.5.1          htmltools_0.5.0        viridis_0.5.1          fansi_0.4.1           
 [13] magrittr_1.5           checkmate_2.0.0        memoise_1.1.0          cluster_2.1.0         
 [17] doParallel_1.0.16      readr_1.4.0            ComplexHeatmap_2.5.4   annotate_1.64.0       
 [21] imputeLCMD_2.0         sandwich_3.0-0         jpeg_0.1-8.1           colorspace_1.4-1      
 [25] blob_1.2.1             xfun_0.19              jsonlite_1.7.1         crayon_1.3.4          
 [29] RCurl_1.98-1.2         genefilter_1.68.0      impute_1.60.0          survival_3.2-7        
 [33] zoo_1.8-8              iterators_1.0.13       glue_1.4.2             gtable_0.3.0          
 [37] zlibbioc_1.32.0        XVector_0.26.0         GetoptLong_1.0.4       shape_1.4.5           
 [41] scales_1.1.1           vsn_3.54.0             mvtnorm_1.1-1          DBI_1.1.0             
 [45] Rcpp_1.0.5             mzR_2.20.0             viridisLite_0.3.0      xtable_1.8-4          
 [49] htmlTable_2.1.0        clue_0.3-57            foreign_0.8-76         bit_4.0.4             
 [53] preprocessCore_1.48.0  Formula_1.2-4          DT_0.16                htmlwidgets_1.5.2     
 [57] RColorBrewer_1.1-2     ellipsis_0.3.1         pkgconfig_2.0.3        XML_3.99-0.3          
 [61] farver_2.0.3           nnet_7.3-14            utf8_1.1.4             locfit_1.5-9.4        
 [65] tidyselect_1.1.0       labeling_0.4.2         rlang_0.4.8            reshape2_1.4.4        
 [69] later_1.1.0.1          AnnotationDbi_1.48.0   munsell_0.5.0          tools_3.6.1           
 [73] cli_2.1.0              generics_0.1.0         RSQLite_2.2.1          evaluate_0.14         
 [77] stringr_1.4.0          fastmap_1.0.1          mzID_1.24.0            yaml_2.2.1            
 [81] knitr_1.30             bit64_4.0.5            purrr_0.3.4            ncdf4_1.17            
 [85] mime_0.9               compiler_3.6.1         rstudioapi_0.11        png_0.1-7             
 [89] affyio_1.56.0          geneplotter_1.64.0     stringi_1.5.3          MSnbase_2.12.0        
 [93] lattice_0.20-41        ProtGenerics_1.18.0    Matrix_1.2-17          tmvtnorm_1.4-10       
 [97] vctrs_0.3.4            pillar_1.4.6           norm_1.0-9.5           lifecycle_0.2.0       
[101] BiocManager_1.30.10    MALDIquant_1.19.3      GlobalOptions_0.1.2    data.table_1.13.2     
[105] bitops_1.0-6           httpuv_1.5.4           R6_2.5.0               latticeExtra_0.6-29   
[109] pcaMethods_1.78.0      affy_1.64.0            promises_1.1.1         gridExtra_2.3         
[113] codetools_0.2-18       MASS_7.3-53            assertthat_0.2.1       DESeq2_1.26.0         
[117] rjson_0.2.20           withr_2.3.0            GenomeInfoDbData_1.2.2 hms_0.5.3             
[121] grid_3.6.1             rpart_4.1-15           tidyr_1.1.2            rmarkdown_2.5         
[125] Cairo_1.5-12.2         base64enc_0.1-3

[ATpoint]

Is your SummarizedExperiment (so the variable you assigned it to) also called SummarizedExperiment? By the way, please stop opening multiple questions with the same content, if you don't get answers then edit it and provide more effort/details. I left the most recent one of those SILAC questions open and closed the rest.

Answer 1

[jared.andrews07]

Issue here is that you don't assign the SummarizedExperiment you create to an actual variable and then just feed the class name to the plot_frequency function.

[yueli7]

Hello Jared.andrew,

Thank yo so much for your great help!

Thank you!

Best,

Yue