Question: DESeq2: Error: $ operator is invalid for atomic vectors using DESeqDataSetFromMatrix
1
Nicolas Rosewick ♦ 7.5k wrote:
Hi,
I want to use DESeq2 to perform some differential expression analysis. I've an expression matrix a2 (raw read count computed using featureCounts) and a design table d2 with two variables ("a" and "b"). When I try to create a deseq2 object using DESeqDataSetFromMatrix, an error appears:
> dds <- DESeqDataSetFromMatrix(a2,d2,"~a+b") Error: $ operator is invalid for atomic vectors
I don't understand why it didn't work. I tried with the pasilla data and it worked perfectly...
Anyone has an idea of the origin of the problem ?
Here are a subset of a2 and d2
a2: count Table
> a2[1:10,] a_1 a_2 a_3 a_4 a_5 a_6 a_7 a_8 a_9 a_10 a_11 a_12 a_13 a_14 a_15 a_16 a_17 a_18 a_19 a_20 a_21 a_22 a_23 a_24 a_25 ENSG00000006459 752 2883 3088 860 2854 1673 4303 2013 0 4345 1863 4743 2474 5609 5741 893 3559 2 2103 1708 6320 4545 2597 1406 1144 ENSG00000015153 287 1101 1448 607 1470 1748 2130 805 0 1347 717 2186 1014 2402 1714 856 1848 2 484 666 1594 1519 580 1499 548 ENSG00000208892 56 438 418 190 787 1022 712 370 0 1410 447 519 292 509 1432 167 173 1 768 340 520 407 147 229 139 ENSG00000110911 231 1072 1478 681 1094 1073 2035 614 0 653 524 873 799 1669 2815 551 1207 1 630 392 1219 1013 957 531 423 ENSG00000127914 1809 4610 4400 3296 10421 7276 7133 3693 0 9658 4708 9817 5072 14495 14322 4699 4222 5 5790 3964 11958 8508 5991 4912 1621 ENSG00000201367 0 23 25 6 52 42 94 43 0 18 16 92 8 40 17 11 10 0 13 11 8 9 8 20 19 ENSG00000221491 68 361 684 184 465 684 524 196 0 631 208 218 408 584 1908 210 260 2 431 174 469 373 217 368 121 ENSG00000271204 51 488 293 177 1150 696 1183 637 0 627 1186 824 356 423 175 135 148 0 330 173 250 339 156 474 385 ENSG00000067560 17478 9436 4175 9112 7122 4130 5550 2073 0 4584 4954 5485 17002 24242 19505 13329 12473 4 2723 2414 10176 22690 23568 15524 2610 ENSG00000136044 427 709 617 559 826 1253 1098 460 0 689 634 1087 787 1859 1485 469 906 2 651 340 1210 1216 744 1014 442
d2: design table with tow variables
> d2 a b a_1 treated old a_2 untreated old a_3 untreated old a_4 treated new a_5 untreated old a_6 untreated old a_7 untreated new a_8 untreated old a_9 untreated old a_10 untreated old a_11 untreated old a_12 untreated old a_13 treated old a_14 untreated old a_15 untreated new a_16 treated new a_17 untreated old a_18 untreated old a_19 untreated old a_20 untreated old a_21 untreated old a_22 treated old a_23 treated old a_24 untreated old a_25 untreated old > sessionInfo() R version 3.1.3 (2015-03-09) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows XP (build 2600) Service Pack 3 locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] pasilla_0.5.1 DESeq_1.18.0 lattice_0.20-30 locfit_1.5-9.1 Biobase_2.26.0 DESeq2_1.6.3 RcppArmadillo_0.5.100.1.0 Rcpp_0.11.6 [9] GenomicRanges_1.18.4 GenomeInfoDb_1.2.5 IRanges_2.0.1 S4Vectors_0.4.0 BiocGenerics_0.12.1 BiocInstaller_1.16.4 loaded via a namespace (and not attached): [1] acepack_1.3-3.3 annotate_1.44.0 AnnotationDbi_1.28.2 base64enc_0.1-2 BatchJobs_1.6 BBmisc_1.9 BiocParallel_1.0.3 brew_1.0-6 checkmate_1.5.2 cluster_2.0.1 codetools_0.2-10 [12] colorspace_1.2-6 DBI_0.3.1 digest_0.6.8 fail_1.2 foreach_1.4.2 foreign_0.8-63 Formula_1.2-1 genefilter_1.48.1 geneplotter_1.44.0 ggplot2_1.0.1 grid_3.1.3 [23] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.16-0 iterators_1.0.7 latticeExtra_0.6-26 magrittr_1.5 MASS_7.3-39 munsell_0.4.2 nnet_7.3-9 plyr_1.8.2 proto_0.3-10 [34] RColorBrewer_1.1-2 reshape2_1.4.1 rpart_4.1-9 RSQLite_1.0.0 scales_0.2.4 sendmailR_1.2-1 splines_3.1.3 stringi_0.4-1 stringr_1.0.0 survival_2.38-1 tools_3.1.3 [45] XML_3.98-1.1 xtable_1.7-4 XVector_0.6.0
