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rr1859 / R.4Cker

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Error in DESeqDataSet(se, design = design, ignoreRank) #61

Closed eandresleon closed 3 years ago

eandresleon commented 3 years ago

Dear,

While using the demo data I obtain an error in the differentialAnalysis step:

This is the comand (coodinates = NULL gives the same error)

res_df = differentialAnalysis(obj=my_obj,
                              norm_counts_avg=nb_results$norm_counts_avg,
                              windows=nb_results$window_counts,
                              conditions=c("DN", "ImmB"),
                              region="nearbait",
                              coordinates=c(41e6,42e6),
                              pval=0.05)

and this is the error:

converting counts to integer mode Error in DESeqDataSet(se, design = design, ignoreRank) : design has a single variable, with all samples having the same value. use instead a design of '~ 1'. estimateSizeFactors, rlog and the VST can then be used

My sessionInfo()

sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats graphics grDevices utils datasets methods base

other attached packages: [1] ggplot2_3.3.2 Rsolnp_1.16 R.4Cker_0.0.0.9000 devtools_2.3.1 usethis_1.6.1

loaded via a namespace (and not attached): [1] colorspace_1.4-1 ellipsis_0.3.1 depmixS4_1.4-2 rprojroot_1.3-2 htmlTable_2.0.1
[6] XVector_0.26.0 GenomicRanges_1.38.0 base64enc_0.1-3 fs_1.5.0 rstudioapi_0.11
[11] farver_2.0.3 remotes_2.2.0 bit64_4.0.2 AnnotationDbi_1.48.0 fansi_0.4.1
[16] splines_3.6.2 mnormt_2.0.2 geneplotter_1.64.0 knitr_1.29 pkgload_1.1.0
[21] Formula_1.2-3 annotate_1.64.0 cluster_2.1.0 png_0.1-7 BiocManager_1.30.10
[26] compiler_3.6.2 backports_1.1.8 assertthat_0.2.1 Matrix_1.2-18 cli_2.0.2
[31] htmltools_0.5.0 prettyunits_1.1.1 tools_3.6.2 gtable_0.3.0 glue_1.4.1
[36] GenomeInfoDbData_1.2.2 dplyr_1.0.1 Rcpp_1.0.5 Biobase_2.46.0 vctrs_0.3.2
[41] nlme_3.1-148 psych_2.0.9 xfun_0.16 stringr_1.4.0 ps_1.3.4
[46] testthat_2.3.2 lifecycle_0.2.0 XML_3.99-0.3 zlibbioc_1.32.0 MASS_7.3-51.6
[51] scales_1.1.1 miscTools_0.6-26 parallel_3.6.2 SummarizedExperiment_1.16.1 RColorBrewer_1.1-2
[56] yaml_2.2.1 curl_4.3 memoise_1.1.0 gridExtra_2.3 rpart_4.1-15
[61] latticeExtra_0.6-29 stringi_1.4.6 RSQLite_2.2.0 genefilter_1.68.0 S4Vectors_0.24.4
[66] desc_1.2.0 checkmate_2.0.0 BiocGenerics_0.32.0 pkgbuild_1.1.0 BiocParallel_1.20.1
[71] truncnorm_1.0-8 GenomeInfoDb_1.22.1 rlang_0.4.7 pkgconfig_2.0.3 matrixStats_0.56.0
[76] bitops_1.0-6 lattice_0.20-41 purrr_0.3.4 labeling_0.3 htmlwidgets_1.5.1
[81] bit_4.0.4 processx_3.4.3 tidyselect_1.1.0 magrittr_1.5 DESeq2_1.26.0
[86] R6_2.4.1 IRanges_2.20.2 generics_0.0.2 Hmisc_4.4-1 DelayedArray_0.12.3
[91] DBI_1.1.0 pillar_1.4.6 foreign_0.8-75 withr_2.2.0 survival_3.2-3
[96] RCurl_1.98-1.2 nnet_7.3-14 tibble_3.0.3 crayon_1.3.4 tmvnsim_1.0-2
[101] jpeg_0.1-8.1 locfit_1.5-9.4 grid_3.6.2 data.table_1.12.8 blob_1.2.1
[106] callr_3.4.3 digest_0.6.25 xtable_1.8-4 stats4_3.6.2 munsell_0.5.0
[111] sessioninfo_1.1.1

eandresleon commented 3 years ago

It seems it works on my Linux desktop ... sorry for the inconvenience