deseq2 problem

Question

[biology_inform]

Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below.

 > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable)  :  unable to find an inherited method for function ‘sizeFactors’ for signature ‘"spec_tbl_df"’

    > DESeq2::plotPCA(eliminated_data,
    +         intgroup = c('WT', 'Resistant'),
    +         returnData = FALSE) Error in (function (classes, fdef, mtable)  :  unable to find an inherited method for function ‘plotPCA’ for signature ‘"spec_tbl_df"’

sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.3

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] dplyr_1.0.8
DESeq2_1.34.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 [5] MatrixGenerics_1.6.0 matrixStats_0.61.0
caroline_0.7.6 edgeR_3.36.0 [9] limma_3.50.3 BiocManager_1.30.16
GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 [13] IRanges_2.28.0 S4Vectors_0.32.4
BiocGenerics_0.40.0 biomaRt_2.50.3

loaded via a namespace (and not attached): [1] httr_1.4.2
bit64_4.0.5 splines_4.1.3 assertthat_0.2.1
[5] BiocFileCache_2.2.1 blob_1.2.3
GenomeInfoDbData_1.2.7 Rsamtools_2.10.0 [9] yaml_2.3.5
progress_1.2.2 pillar_1.7.0 RSQLite_2.2.12
[13] lattice_0.20-45 glue_1.6.2 digest_0.6.29
RColorBrewer_1.1-3 [17] XVector_0.34.0
colorspace_2.0-3 Matrix_1.4-1 XML_3.99-0.9
[21] pkgconfig_2.0.3 genefilter_1.76.0 zlibbioc_1.40.0 xtable_1.8-4 [25] purrr_0.3.4 scales_1.1.1
BiocParallel_1.28.3 annotate_1.72.0 [29] tibble_3.1.6
KEGGREST_1.34.0 ggplot2_3.3.5 generics_0.1.2
[33] ellipsis_0.3.2 cachem_1.0.6 cli_3.2.0
survival_3.3-1 [37] magrittr_2.0.3 crayon_1.5.1
memoise_2.0.1 fansi_1.0.3 [41] xml2_1.3.3
tools_4.1.3 prettyunits_1.1.1 hms_1.1.1
[45] BiocIO_1.4.0 lifecycle_1.0.1 stringr_1.4.0
munsell_0.5.0 [49] locfit_1.5-9.5
DelayedArray_0.20.0 AnnotationDbi_1.56.2 Biostrings_2.62.0
[53] compiler_4.1.3 rlang_1.0.2 grid_4.1.3
RCurl_1.98-1.6 [57] rstudioapi_0.13 rjson_0.2.21
rappdirs_0.3.3 bitops_1.0-7 [61] gtable_0.3.0
restfulr_0.0.13 DBI_1.1.2 curl_4.3.2
[65] R6_2.5.1 GenomicAlignments_1.30.0 rtracklayer_1.54.0 fastmap_1.1.0 [69] bit_4.0.4
utf8_1.2.2 filelock_1.0.2 stringi_1.7.6
[73] parallel_4.1.3 Rcpp_1.0.8.3
geneplotter_1.72.0 vctrs_0.4.0 [77] png_0.1-7
dbplyr_2.1.1 tidyselect_1.1.2

I couldnt figure out why is this happening? Thanks in advance

[cpad0112]

cross posted at https://support.bioconductor.org/p/9143383/ and addressed.