rnaseqDTU Workflow, Precision estimation error.
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Entering edit mode
@dixitanirudha-23596
Last seen 17 months ago

Hi, I have a Arabidopsis, paired-ended, RNA seq dateset with 4 conditions (1 control, 3 treatments). I have been following the rnaseqDTU paper (https://f1000research.com/articles/7-952/v3) and the R code within. I was able to follow all the steps until the following,

> set.seed(1)
> system.time({
+   d_1500 <- dmPrecision(d_filtered, design=design_full)
+   d_1500 <- dmFit(d_filtered, design=design_full)
+   d_1500 <- dmTest(d_filtered, coef="condition1500")
+ })
! Using a subset of 0.1 genes to estimate common precision !

! Using common_precision = 13.1556 as prec_init !

! Using 0.956883 as a shrinkage factor !

    Error in (function (classes, fdef, mtable)  : 
      unable to find an inherited method for function 'dmFit' for signature '"dmDSdata"' 
    Timing stopped at: 612.8 141.1 590.3 

I am by no means an expert at these kinds of analysis but I did check the sessionInfo() output to make sure that required packages are loaded. Ultimately, I am not sure what the above error means or how can I resolve it.

    R version 3.6.3 (2020-02-29)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: Linux Mint 19.2

    Matrix products: default
    BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
    LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

    locale:
     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
     [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

    other attached packages:
     [1] ensembldb_2.10.2            AnnotationFilter_1.10.0     GenomicFeatures_1.38.2      tximport_1.14.2             rnaseqDTU_1.6.0            
     [6] devtools_2.3.0              usethis_1.6.1               rafalib_1.0.0               edgeR_3.28.1                limma_3.42.2               
    [11] stageR_1.8.0                DEXSeq_1.32.0               RColorBrewer_1.1-2          AnnotationDbi_1.48.0        DESeq2_1.26.0              
    [16] SummarizedExperiment_1.16.1 DelayedArray_0.12.3         matrixStats_0.56.0          GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
    [21] IRanges_2.20.2              S4Vectors_0.24.4            Biobase_2.46.0              BiocGenerics_0.32.0         BiocParallel_1.20.1        
    [26] DRIMSeq_1.14.0             

    loaded via a namespace (and not attached):
      [1] colorspace_1.4-1         hwriter_1.3.2            ellipsis_0.3.1           rprojroot_1.3-2          htmlTable_1.13.3         XVector_0.26.0          
      [7] base64enc_0.1-3          fs_1.4.1                 rstudioapi_0.11          remotes_2.1.1            bit64_0.9-7              fansi_0.4.1             
     [13] splines_3.6.3            geneplotter_1.64.0       knitr_1.28               pkgload_1.0.2            Formula_1.2-3            Rsamtools_2.2.3         
     [19] annotate_1.64.0          cluster_2.1.0            dbplyr_1.4.3             png_0.1-7                compiler_3.6.3           httr_1.4.1              
     [25] backports_1.1.7          lazyeval_0.2.2           assertthat_0.2.1         Matrix_1.2-18            cli_2.0.2                acepack_1.4.1           
     [31] htmltools_0.4.0          prettyunits_1.1.1        tools_3.6.3              gtable_0.3.0             glue_1.4.1               GenomeInfoDbData_1.2.2  
     [37] reshape2_1.4.4           dplyr_0.8.5              rappdirs_0.3.1           Rcpp_1.0.4.6             vctrs_0.3.0              Biostrings_2.54.0       
     [43] rtracklayer_1.46.0       xfun_0.14                stringr_1.4.0            ps_1.3.3                 testthat_2.3.2           lifecycle_0.2.0         
     [49] statmod_1.4.34           XML_3.99-0.3             zlibbioc_1.32.0          scales_1.1.1             ProtGenerics_1.18.0      hms_0.5.3               
     [55] curl_4.3                 memoise_1.1.0            gridExtra_2.3            ggplot2_3.3.0            biomaRt_2.42.1           rpart_4.1-15            
     [61] latticeExtra_0.6-29      stringi_1.4.6            RSQLite_2.2.0            genefilter_1.68.0        desc_1.2.0               checkmate_2.0.0         
     [67] pkgbuild_1.0.8           rlang_0.4.6              pkgconfig_2.0.3          bitops_1.0-6             lattice_0.20-41          purrr_0.3.4             
     [73] GenomicAlignments_1.22.1 htmlwidgets_1.5.1        processx_3.4.2           bit_1.1-15.2             tidyselect_1.1.0         plyr_1.8.6              
     [79] magrittr_1.5             R6_2.4.1                 Hmisc_4.4-0              DBI_1.1.0                withr_2.2.0              pillar_1.4.4            
     [85] foreign_0.8-76           survival_3.1-12          RCurl_1.98-1.2           nnet_7.3-14              tibble_3.0.1             crayon_1.3.4            
     [91] BiocFileCache_1.10.2     jpeg_0.1-8.1             progress_1.2.2           locfit_1.5-9.4           grid_3.6.3               data.table_1.12.8       
     [97] blob_1.2.1               callr_3.4.3              digest_0.6.25            xtable_1.8-4             openssl_1.4.1            munsell_0.5.0           
    [103] sessioninfo_1.1.1        askpass_1.1 

Any advice/suggestion to resolve this will be great. Thank you very much for your time and consideration.

rnaseqDTU • 160 views
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Entering edit mode
@mikelove
Last seen 3 hours ago
United States

Take a closer look at the DRIMSeq section:

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html#drimseq

d <- dmPrecision(d, design=design_full)
d <- dmFit(d, design=design_full)
d <- dmTest(d, coef="condition2")

Note that d is passed through these functions, from the input to the output, which becomes the input of the next function. Above you are not passing the object through the functions but starting again with your initial object.

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Entering edit mode

Ahhh..thank you very much for pointing it out....it was right there. Appreciated.

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