Entering edit mode
4.1 years ago
yueli7
▴
250
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
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.