Entering edit mode
Bio
•
0
@bio-23985
Last seen 2 days ago
The code that used to work in R 3.6.1 is giving me an error in R 4.0. The exact error is discussed in the github thread at github/Bioconductor/SummarizedExperiment/ but I have trouble understanding how to address the issue based on the discussion there. The culprit is the following line:
DESeqDataSetFromMatrix(countData=RNASeqCnts$counts, colData=cData, design=~sex+group)
Which gives the error:
Error in `assays<-`(`*tmp*`, withDimnames = withDimnames, ..., value = `*vtmp*`) : please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x, withDimnames=FALSE)) <- value' when the dimnames on the supplied assay(s) are not identical to the dimnames on RangedSummarizedExperiment object 'x'
The variablle RNASeqCnts$counts is the output of the ReadsPerGene files from STAR. Head of the file looks like this:
Samples
Tags PM10LTA PM11LTA PM12LTA PM14LTA PM17RTA PM1LTA PM21LTA
ENSMUSG1 0 0 0 0 0 0 0
ENSMUSG2 0 0 0 0 0 0 0
ENSMUSG3 0 0 2 0 0 0 0
ENSMUSG4 0 0 0 0 0 0 0
Please let me know if dim() information is also needed, and for which variables if that would help. I have included both sessionInfos at the end.
Thank you.
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.10 (Santiago)
Matrix products: default
BLAS: /share/pkg/R/4.0.0_gcc/lib64/R/lib/libRblas.so
LAPACK: /share/pkg/R/4.0.0_gcc/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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] biomaRt_2.46.0 dplyr_1.0.2
[3] edgeR_3.32.0 limma_3.46.0
[5] DESeq2_1.30.0 SummarizedExperiment_1.20.0
[7] Biobase_2.50.0 MatrixGenerics_1.2.0
[9] matrixStats_0.57.0 GenomicRanges_1.42.0
[11] GenomeInfoDb_1.26.2 IRanges_2.24.1
[13] S4Vectors_0.28.1 BiocGenerics_0.36.0
[15] WGCNA_1.69 fastcluster_1.1.25
[17] dynamicTreeCut_1.63-1
loaded via a namespace (and not attached):
[1] bitops_1.0-6 bit64_4.0.5 progress_1.2.2
[4] doParallel_1.0.15 RColorBrewer_1.1-2 httr_1.4.2
[7] tools_4.0.0 backports_1.2.1 R6_2.5.0
[10] rpart_4.1-15 Hmisc_4.4-2 DBI_1.1.0
[13] colorspace_2.0-0 nnet_7.3-14 prettyunits_1.1.1
[16] tidyselect_1.1.0 gridExtra_2.3 curl_4.3
[19] bit_4.0.4 compiler_4.0.0 preprocessCore_1.52.0
[22] htmlTable_2.1.0 xml2_1.3.2 DelayedArray_0.16.0
[25] scales_1.1.1 checkmate_2.0.0 genefilter_1.72.0
[28] askpass_1.1 rappdirs_0.3.1 stringr_1.4.0
[31] digest_0.6.25 foreign_0.8-78 XVector_0.30.0
[34] base64enc_0.1-3 jpeg_0.1-8.1 pkgconfig_2.0.3
[37] htmltools_0.5.0 dbplyr_2.0.0 htmlwidgets_1.5.1
[40] rlang_0.4.8 rstudioapi_0.11 RSQLite_2.2.1
[43] impute_1.64.0 generics_0.1.0 BiocParallel_1.24.1
[46] RCurl_1.98-1.2 magrittr_1.5 GO.db_3.12.1
[49] GenomeInfoDbData_1.2.4 Formula_1.2-4 Matrix_1.2-18
[52] Rcpp_1.0.5 munsell_0.5.0 lifecycle_0.2.0
[55] stringi_1.4.6 zlibbioc_1.36.0 BiocFileCache_1.14.0
[58] grid_4.0.0 blob_1.2.1 crayon_1.3.4
[61] lattice_0.20-41 splines_4.0.0 annotate_1.68.0
[64] hms_0.5.3 locfit_1.5-9.4 knitr_1.28
[67] pillar_1.4.4 geneplotter_1.68.0 codetools_0.2-18
[70] XML_3.99-0.5 glue_1.4.1 latticeExtra_0.6-29
[73] data.table_1.13.6 png_0.1-7 vctrs_0.3.5
[76] foreach_1.5.0 openssl_1.4.1 gtable_0.3.0
[79] purrr_0.3.4 assertthat_0.2.1 ggplot2_3.3.3
[82] xfun_0.14 xtable_1.8-4 survival_3.1-12
[85] tibble_3.0.1 iterators_1.0.12 AnnotationDbi_1.52.0
[88] memoise_1.1.0 cluster_2.1.0 ellipsis_0.3.1
I tried running the suggested BiocManager::install() but I always end up with these packages installing with a non-zero status. Is any of them needed for DESeq2?
This could explain the error you are seeing, but if you want to just fix the error without dealing with installation, you can try my alternative approach (remove conflicting names).
Thank you!