Entering edit mode
929072397
•
0
@929072397-15330
Last seen 6.0 years ago
Hi, everyone,
I'm running this line in DESeq2 1.18.1
dds1<-DESeqDataSetFromMatrix(countData = countdata1,colData = coldata1,design= ~ day+treatment)
but a error happened:
Error in if (assays_nrow != rowData_nrow) { : argument is of length zero.
Why this happen? I have run this line many times and it is OK previously.
This is my countdata1 and coldata1:
head(coldata1) day treatment specific M1D0 0 Pulse_AgNP 0_Pulse_AgNP M1D1 1 Pulse_AgNP 1_Pulse_AgNP M1D3 3 Pulse_AgNP 3_Pulse_AgNP M1D7 7 Pulse_AgNP 7_Pulse_AgNP M1D14 14 Pulse_AgNP 14_Pulse_AgNP M1D28 28 Pulse_AgNP 28_Pulse_AgNP head(countdata1) M1D0 M1D1 M1D3 M1D7 M1D14 M1D28 M1D98 M1D126 M1D203 M1D273 M1D330 M1D364 M2D0 M2D1 M2D3 OTU_6 278673 17123 1004 2095 626380 77239 0 0 397 163044 509196 68142 7962 5299 5280 OTU_19 1203 0 0 0 0 937508 34179 0 44977 355505 387525 257265 4993 1342 1738 OTU_2 62826 0 0 274 100277 246938 248305 5420 181724 95374 46374 391341 270635 3524 3470 OTU_1 3161 1534582 1812810 34913 0 0 0 0 0 0 0 0 5580 83355 100648 OTU_3 1112313 19966 0 557619 142265 89957 2742 0 3740 64226 140615 109204 9936 3505 62165 OTU_4 72835 5643 0 0 0 37732 100159 47225 214901 70906 9343 66331 101244 49405 255815 M2D7 M2D14 M2D28 M2D98 M2D126 M2D203 M2D273 M2D330 M2D364 M4D0 M4D1 M4D3 M4D7 M4D14 M4D28 M4D98 OTU_6 917 11980 71046 0 0 0 238108 94303 324842 991990 125947 167798 377852 787716 476976 0 OTU_19 395554 75254 81272 42580 907 224528 104372 739969 250072 0 0 0 0 0 798 0 OTU_2 18089 19281 118060 348372 19282 200200 46904 334915 181795 4418 0 336 0 19017 67724 56881 OTU_1 0 0 197 0 0 0 304 0 0 0 27745 379477 3329 0 0 0 OTU_3 412329 510225 307706 53054 2351 0 119184 105990 18294 0 0 713 0 45043 294026 1572 OTU_4 241904 70083 98436 44923 113886 3690 279220 24777 288650 196250 35663 56211 141811 116604 3144 0
And the sessioninfo:
sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq2_1.18.1 SummarizedExperiment_1.8.1 DelayedArray_0.4.1 matrixStats_0.53.1 [5] Biobase_2.38.0 GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 IRanges_2.12.0 [9] S4Vectors_0.16.0 BiocGenerics_0.24.0 loaded via a namespace (and not attached): [1] genefilter_1.60.0 locfit_1.5-9.1 splines_3.4.4 lattice_0.20-35 colorspace_1.3-2 [6] htmltools_0.3.6 yaml_2.1.18 base64enc_0.1-3 blob_1.1.0 survival_2.41-3 [11] XML_3.98-1.10 rlang_0.2.0 pillar_1.2.1 DBI_0.8 foreign_0.8-69 [16] BiocParallel_1.12.0 bit64_0.9-7 RColorBrewer_1.1-2 GenomeInfoDbData_1.0.0 plyr_1.8.4 [21] stringr_1.3.0 zlibbioc_1.24.0 munsell_0.4.3 gtable_0.2.0 htmlwidgets_1.0 [26] memoise_1.1.0 latticeExtra_0.6-28 knitr_1.20 geneplotter_1.56.0 AnnotationDbi_1.40.0 [31] htmlTable_1.11.2 Rcpp_0.12.16 acepack_1.4.1 xtable_1.8-2 scales_0.5.0 [36] backports_1.1.2 checkmate_1.8.5 Hmisc_4.1-1 annotate_1.56.1 XVector_0.18.0 [41] bit_1.1-12 gridExtra_2.3 ggplot2_2.2.1 digest_0.6.15 stringi_1.1.7 [46] grid_3.4.4 tools_3.4.4 bitops_1.0-6 magrittr_1.5 RSQLite_2.0 [51] lazyeval_0.2.1 RCurl_1.95-4.10 tibble_1.4.2 Formula_1.2-2 cluster_2.0.6 [56] Matrix_1.2-12 data.table_1.10.4-3 rstudioapi_0.7 rpart_4.1-13 nnet_7.3-12 [61] compiler_3.4.4
Thank for any help!
Oliver