Closed soobeomlee closed 3 years ago
rj-patrick
commented
3 years ago Hi @soobeomlee,
Can you confirm whether you are able to run the example in the vignette without error?
Would you be able to show the command that you are running and any other text printed by DUTest?
Cheers, Ralph
soobeomlee
commented
3 years ago Hi, thanks for the quick reply. I ran the example in the vignette and got the same error. I believe the version difference of some package might be a problem. I will try to reinstall and run. please let me know when you get a hint for this issue.
FYI, here's traceback.
traceback()
11: stop(gettextf("assignment of an object of class %s is not valid for slot %s in an object of class %s; is(value, \"%s\") is not TRUE",
dQuote(valueClass), sQuote(name), dQuote(cl), slotClass),
domain = NA)
10: checkSlotAssignment(object, name, value)
9: slot<-(*tmp*, what, value = slot(value, what))
8: asMethod(object, Class, value)
7: as<-(*tmp*, Classi, value = obj)
6: initialize(value, ...)
5: initialize(value, ...)
4: new("DEXSeqResults", LRTresults, modelFrameBM = object@modelFrameBM,
sampleData = sampleAnnotation(object), dispersionFunction = object@dispersionFunction)
3: DEXSeq::DEXSeqResults(dxd)
2: apply_DEXSeq_test_seurat(apa.seurat.object = peaks.object, population.1 = population.1,
population.2 = population.2, exp.thresh = exp.thresh, fc.thresh = fc.thresh,
adj.pval.thresh = adj.pval.thresh, num.splits = num.splits,
seed.use = seed.use, feature.type = feature.type, include.annotations = include.annotations,
filter.pA.stretch = filter.pA.stretch, verbose = verbose,
do.MAPlot = do.MAPlot, return.dexseq.res = return.dexseq.res,
ncores = ncores)
1: DUTest(peaks.seurat, population.1 = "F-SL", population.2 = "EC1",
exp.thresh = 0.1, feature.type = c("UTR3", "exon"))
rj-patrick
commented
3 years ago Hi @soobeomlee,
Sorry for the slow response. I have tried running Sierra using the same software versions for the main requirements (DEXSeq version 1.36), Seurat v4 and don't have any issues. Only possibility I can think of is whether there is a conflict between your R and Bioconductor versions. I don't know how likely this is to be a problem, but it appears you are using Bioconductor version 3.12, which is supposed to be for R version 4.03, so I wonder if you were to downgrade to version 3.11 (or upgrade your R version) whether this would solve the issue?
soobeomlee
commented
3 years ago Awesome! It works on Bioconductor 3.11!
Thanks a lot!
rj-patrick
commented
3 years ago No worries, let us know if you have any more issues.
Hi Developers,
Thanks for this cool method.
I'm currently encountering an error when I run DUTest with a Seurat object. The error message is as follows.
[1] "Running DEXSeq test..." Error in checkSlotAssignment(object, name, value) : assignment of an object of class "DFrame" is not valid for slot 'elementMetadata' in an object of class "DEXSeqResults"; is(value, "DataTable_OR_NULL") is not TRUE In addition: Warning message: In DESeqDataSet(rse, design, ignoreRank = TRUE) : some variables in design formula are characters, converting to factors
Can I get some advice to resolve it?
Thanks!
Best, Soobeom
Matrix products: default BLAS: /gpfs/share/apps/R/4.0.0/lib64/R/lib/libRblas.so LAPACK: /gpfs/share/apps/R/4.0.0/lib64/R/lib/libRlapack.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] stringr_1.4.0 Sierra_0.99.24 SeuratObject_4.0.0 Seurat_4.0.0
loaded via a namespace (and not attached): [1] reticulate_1.18 tidyselect_1.1.0
[3] RSQLite_2.2.3 AnnotationDbi_1.52.0
[5] htmlwidgets_1.5.3 grid_4.0.0
[7] BiocParallel_1.24.1 Rtsne_0.15
[9] munsell_0.5.0 codetools_0.2-18
[11] ica_1.0-2 statmod_1.4.35
[13] future_1.21.0 miniUI_0.1.1.1
[15] colorspace_2.0-0 Biobase_2.50.0
[17] knitr_1.31 rstudioapi_0.13
[19] stats4_4.0.0 SingleCellExperiment_1.12.0 [21] ROCR_1.0-11 tensor_1.5
[23] listenv_0.8.0 MatrixGenerics_1.2.0
[25] GenomeInfoDbData_1.2.4 harmony_1.0
[27] hwriter_1.3.2 polyclip_1.10-0
[29] bit64_4.0.5 parallelly_1.23.0
[31] vctrs_0.3.6 generics_0.1.0
[33] xfun_0.20 biovizBase_1.38.0
[35] BiocFileCache_1.14.0 R6_2.5.0
[37] GenomeInfoDb_1.26.2 locfit_1.5-9.4
[39] AnnotationFilter_1.14.0 bitops_1.0-6
[41] spatstat.utils_2.0-0 cachem_1.0.1
[43] DelayedArray_0.16.1 assertthat_0.2.1
[45] promises_1.1.1 scales_1.1.1
[47] nnet_7.3-14 gtable_0.3.0
[49] globals_0.14.0 goftest_1.2-2
[51] ensembldb_2.14.0 rlang_0.4.10
[53] genefilter_1.72.1 splines_4.0.0
[55] rtracklayer_1.50.0 lazyeval_0.2.2
[57] dichromat_2.0-0 checkmate_2.0.0
[59] reshape2_1.4.4 abind_1.4-5
[61] GenomicFeatures_1.42.1 backports_1.2.1
[63] httpuv_1.5.5 Hmisc_4.4-2
[65] tools_4.0.0 ggplot2_3.3.3
[67] ellipsis_0.3.1 RColorBrewer_1.1-2
[69] BiocGenerics_0.36.0 ggridges_0.5.3
[71] Rcpp_1.0.6 plyr_1.8.6
[73] base64enc_0.1-3 progress_1.2.2
[75] zlibbioc_1.36.0 purrr_0.3.4
[77] RCurl_1.98-1.2 prettyunits_1.1.1
[79] rpart_4.1-15 openssl_1.4.3
[81] deldir_0.2-9 pbapply_1.4-3
[83] cowplot_1.1.1 S4Vectors_0.28.1
[85] zoo_1.8-8 SummarizedExperiment_1.20.0 [87] ggrepel_0.9.1 cluster_2.1.0
[89] magrittr_2.0.1 data.table_1.13.6
[91] scattermore_0.7 lmtest_0.9-38
[93] RANN_2.6.1 ProtGenerics_1.22.0
[95] fitdistrplus_1.1-3 matrixStats_0.57.0
[97] hms_1.0.0 patchwork_1.1.1
[99] mime_0.9 xtable_1.8-4
[101] XML_3.99-0.5 jpeg_0.1-8.1
[103] IRanges_2.24.1 gridExtra_2.3
[105] compiler_4.0.0 biomaRt_2.46.2
[107] tibble_3.0.6 KernSmooth_2.23-18
[109] crayon_1.3.4 htmltools_0.5.1.1
[111] mgcv_1.8-33 later_1.1.0.1
[113] Formula_1.2-4 geneplotter_1.68.0
[115] tidyr_1.1.2 DBI_1.1.1
[117] dbplyr_2.0.0 MASS_7.3-53
[119] rappdirs_0.3.2 Matrix_1.2-18
[121] parallel_4.0.0 Gviz_1.34.0
[123] igraph_1.2.6 GenomicRanges_1.42.0
[125] pkgconfig_2.0.3 GenomicAlignments_1.26.0
[127] foreign_0.8-80 plotly_4.9.3
[129] xml2_1.3.2 foreach_1.5.1
[131] annotate_1.68.0 XVector_0.30.0
[133] DEXSeq_1.36.0 VariantAnnotation_1.36.0
[135] digest_0.6.27 sctransform_0.3.2
[137] RcppAnnoy_0.0.18 spatstat.data_1.7-0
[139] Biostrings_2.58.0 leiden_0.3.6
[141] htmlTable_2.1.0 uwot_0.1.10
[143] curl_4.3 shiny_1.6.0
[145] Rsamtools_2.6.0 lifecycle_0.2.0
[147] nlme_3.1-151 jsonlite_1.7.2
[149] viridisLite_0.3.0 askpass_1.1
[151] BSgenome_1.58.0 pillar_1.4.7
[153] lattice_0.20-41 fastmap_1.1.0
[155] httr_1.4.2 survival_3.2-7
[157] glue_1.4.2 spatstat_1.64-1
[159] png_0.1-7 iterators_1.0.13
[161] bit_4.0.4 stringi_1.5.3
[163] blob_1.2.1 DESeq2_1.30.0
[165] latticeExtra_0.6-29 memoise_2.0.0
[167] dplyr_1.0.3 irlba_2.3.3
[169] future.apply_1.7.0