DESeq2
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@da307361
Last seen 1 day ago
Turkey

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

DESeq2 • 124 views
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2
Entering edit mode
Basti ▴ 280
@7d45153c
Last seen 12 hours ago
France

eliminated_data should be "a DESeqDataSet, or matrix of counts" (https://rdrr.io/bioc/DESeq2/man/rlog.html) and not a "spec_tbl_df" object. Please pay attention to your precedent code lines to obtain the desired output

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