Entering edit mode
7.0 years ago
Nicolas Rosewick
9.8k
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
> dds <- DESeqDataSetFromMatrix(a2,d2,~a+b)
Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
That looks better. The warning is about the dataframe (d2), which apparently is using characters rather than factors.
thanks it works