Entering edit mode
I have installed DESeq2 version 1.36.0
samples <- colnames(txi$counts)
group <- as.factor(c("control","control","control","control","control","diet","diet","diet","diet","diet",
"control","control","control","control","control","diet","diet","diet","diet","diet","diet"))
coldata <- data.frame(samples,
group,
stringsAsFactors = F)
coldata <- coldata[,c("samples","group")]
coldata$samples <- factor(coldata$samples)
coldata$group <- factor(coldata$group)
rownames(coldata) <- sub("fb", "", rownames(coldata))
all(rownames(coldata$samples) %in% colnames(txi))
all(rownames(coldata) == colnames(txi))
TRUE
library(DESeq2)
ddsTxi <- DESeqDataSetFromTximport(txi,
colData = coldata,
design = ~ group)
I get in the final line:
Error in SummarizedExperiment(assays = SimpleList(counts = countData), :
the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExperiment object
(or derivative) to construct
4. stop(wmsg("the ", what, " of the supplied assay(s) must be NULL ", "or identical to those of the ", class(ans), " object ", "(or derivative) to construct"))
3. SummarizedExperiment(assays = SimpleList(counts = countData), colData = colData, ...)
2.DESeqDataSetFromMatrix(countData = counts, colData = colData, design = design, ...)
1.DESeqDataSetFromTximport(txi, colData = coldata, design = ~group) > sessionInfo( )
> sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq2_1.36.0 SummarizedExperiment_1.26.0 MatrixGenerics_1.8.0 matrixStats_0.62.0 GenomicRanges_1.48.0
[6] GenomeInfoDb_1.32.1 IRanges_2.30.0 S4Vectors_0.34.0 tximportData_1.24.0 readr_2.1.2
[11] edgeR_3.38.0 limma_3.52.0 dplyr_1.0.8 magrittr_2.0.3 tximport_1.24.0
[16] biomaRt_2.52.0 GEOquery_2.64.0 Biobase_2.56.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached):
[1] Mus.musculus_1.3.1 rappdirs_0.3.3 rtracklayer_1.55.4
[4] ggthemes_4.2.4 Glimma_2.6.0 tidyr_1.2.0
[7] ggplot2_3.3.5 bit64_4.0.5 knitr_1.39
[10] irlba_2.3.5 DelayedArray_0.22.0 data.table_1.14.2
[13] rpart_4.1.16 hwriter_1.3.2.1 KEGGREST_1.36.0
[16] RCurl_1.98-1.6 AnnotationFilter_1.20.0 generics_0.1.2
[19] GenomicFeatures_1.48.0 org.Mm.eg.db_3.15.0 preprocessCore_1.58.0
[22] ScaledMatrix_1.4.0 RSQLite_2.2.12 bit_4.0.4
[25] tzdb_0.3.0 webshot_0.5.3 lubridate_1.8.0
[28] xml2_1.3.3 assertthat_0.2.1 tidyverse_1.3.1
[31] viridis_0.6.2 oligo_1.60.0 xfun_0.30
[34] hms_1.1.1 evaluate_0.15 fansi_1.0.3
[37] restfulr_0.0.13 progress_1.2.2 readxl_1.4.0
[40] dbplyr_2.1.1 igraph_1.3.1 DBI_1.1.2
[43] geneplotter_1.74.0 htmlwidgets_1.5.4 purrr_0.3.4
[46] ellipsis_0.3.2 backports_1.4.1 hgu95acdf_2.18.0
[49] annotate_1.74.0 sparseMatrixStats_1.8.0 vctrs_0.4.1
[52] SingleCellExperiment_1.18.0 ensembldb_2.20.0 abind_1.4-5
[55] beadarray_2.46.0 withr_2.5.0 cachem_1.0.6
[58] gcrma_2.68.0 vroom_1.5.7 checkmate_2.1.0
[61] GenomicAlignments_1.32.0 prettyunits_1.1.1 scran_1.24.0
[64] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 svglite_2.1.0 cluster_2.1.3
[67] lazyeval_0.2.2 crayon_1.5.1 genefilter_1.78.0
[70] pkgconfig_2.0.3 vipor_0.4.5 ProtGenerics_1.28.0
[73] nnet_7.3-17 rlang_1.0.2 ecolicdf_2.18.0
[76] lifecycle_1.0.1 SpikeInSubset_1.36.0 filelock_1.0.2
[79] BeadDataPackR_1.48.0 affyio_1.66.0 ALLMLL_1.36.0
[82] BiocFileCache_2.4.0 modelr_0.1.8 rsvd_1.0.5
[85] cellranger_1.1.0 graph_1.74.0 base64_2.0
[88] Matrix_1.4-1 carData_3.0-5 hgu133bcdf_2.18.0
[91] affyPLM_1.71.0 reprex_2.0.1 base64enc_0.1-3
[94] beeswarm_0.4.0 png_0.1-7 viridisLite_0.4.0
[97] rjson_0.2.21 bitops_1.0-7 hgu133plus2cdf_2.18.0
[100] Biostrings_2.64.0 blob_1.2.3 DelayedMatrixStats_1.18.0
[103] stringr_1.4.0 jpeg_0.1-9 beachmat_2.12.0
[106] scales_1.2.0 memoise_2.0.1 plyr_1.8.7
[109] hexbin_1.28.2 zlibbioc_1.42.0 compiler_4.2.0
[112] factoextra_1.0.7 kableExtra_1.3.4 dqrng_0.3.0
[115] BiocIO_1.6.0 RColorBrewer_1.1-3 illuminaio_0.38.0
[118] Rsamtools_2.12.0 cli_3.3.0 affy_1.74.0
[121] XVector_0.36.0 oligoClasses_1.58.0 htmlTable_2.4.0
[124] Formula_1.2-4 MASS_7.3-56 hgu95av2.db_3.13.0
[127] tidyselect_1.1.2 vsn_3.64.0 forcats_0.5.1
[130] stringi_1.7.6 mouse4302cdf_2.18.0 yaml_2.3.5
[133] BiocSingular_1.12.0 askpass_1.1 locfit_1.5-9.5
[136] latticeExtra_0.6-29 ggrepel_0.9.1 grid_4.2.0
[139] tools_4.2.0 soybeancdf_2.18.0 parallel_4.2.0
[142] rstudioapi_0.13 bluster_1.6.0 foreach_1.5.2
[145] foreign_0.8-82 metapod_1.4.0 arrayQualityMetrics_3.52.0
[148] gridExtra_2.3 Rtsne_0.16 digest_0.6.29
[151] BiocManager_1.30.17 ff_4.0.5 Rcpp_1.0.8.3
[154] car_3.0-12 broom_0.8.0 setRNG_2022.4-1
[157] scuttle_1.6.0 pd.hg.u133.plus.2_3.12.0 OrganismDbi_1.38.0
[160] httr_1.4.2 AnnotationDbi_1.58.0 colorspace_2.0-3
[163] rvest_1.0.2 fs_1.5.2 XML_3.99-0.9
[166] splines_4.2.0 statmod_1.4.36 RBGL_1.72.0
[169] scater_1.24.0 multtest_2.52.0 ArrayExpress_1.56.0
[172] systemfonts_1.0.4 xtable_1.8-4 jsonlite_1.8.0
[175] R6_2.5.1 Hmisc_4.7-0 pillar_1.7.0
[178] htmltools_0.5.2 affxparser_1.68.0 glue_1.6.2
[181] fastmap_1.1.0 BiocParallel_1.30.0 BiocNeighbors_1.14.0
[184] gridSVG_1.7-4 codetools_0.2-18 utf8_1.2.2
[187] lattice_0.20-45 tibble_3.1.6 curl_4.3.2
[190] ggbeeswarm_0.6.0 ggfortify_0.4.14 GO.db_3.15.0
[193] openssl_2.0.0 survival_3.3-1 rmarkdown_2.14
[196] ecoliLeucine_1.36.0 munsell_0.5.0 GenomeInfoDbData_1.2.8
[199] iterators_1.0.14 haven_2.5.0 reshape2_1.4.4
[202] gtable_0.3.0
Thank you, the labels are the same. Also it has runned once randomly when running line per line, I've tried again but get the error every time
The error is from SummarizedExperiment, and it won't return as an error if the labels were the same -- it's not stochastic. It's just an internal check in SummarizedExperiment, that you don't have mislabelled colData.
Thank you, but when I run:
it returns TRUE, next also some more information about the variables, where would the mistake be then?
Your
all(rownames(coldata) == colnames(txi))results in NULL which is expected becausetxiis a list and lists do not have rownames. Be also careful withall(), it returns TRUE if you compare anything toNULL, likeall(NULL=="foo"). What you must check is thatcolnames(txi$counts) == rownames(colData)and that is likely not the case. Better useidentical()rather thanall(), as the above behaviour of returning TRUE is one annoying pitfall of that function.Yes indeed thanks! This is what I get:
Then what do I need to change so that the function runs on my system?
Sorry corrected version: