perishky
commented
2 years ago Sorry about the wait, just realized I had missed this back in December.
The problem is due to deriving surrogate variables in such a small dataset. The error should be fixed if in the call to ewaff.sites() you add the following arguments: random.subset=1 n.confounders=1 The first argument says to use the full dataset to generate surrogate variables. For large datasets, SVA can be really slow so we generate surrogate variables from a subset. The second argument says to generate only one surrogate variable.
Hi Matthew,
I installed your package and i using your data fro the tutorial, same seed and following line by line
However, when i arrive to that particular line
sites.ret <- ewaff.sites(methylation ~ variable + continuous + categorical, variable.of.interest="variable", methylation=methylation, data=data, generate.confounders="sva", method="glm")
I got Error in uu$d[1:ndf] : only 0's may be mixed with negative subscripts
this is my sessionInfo
R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS
Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] ewaff_0.0.2 metafor_2.1-0 Matrix_1.2-17 mice_3.12.0 survival_3.1-8 sandwich_2.5-1 lmtest_0.9-37
[8] zoo_1.8-6 MASS_7.3-51.5 limma_3.40.6 markdown_1.1 knitr_1.26 SmartSVA_0.1.3 RSpectra_0.16-0
[15] isva_1.9 JADE_2.0-3 fastICA_1.2-2 qvalue_2.16.0 sva_3.32.1 BiocParallel_1.18.1 genefilter_1.66.0
[22] mgcv_1.8-31 nlme_3.1-142 ggplot2_3.3.2
loaded via a namespace (and not attached): [1] tidyselect_1.0.0 htmlwidgets_1.5.1 RSQLite_2.1.5 AnnotationDbi_1.46.1 FactoMineR_2.1
[6] grid_3.6.1 Rtsne_0.15 munsell_0.5.0 codetools_0.2-16 preprocessCore_1.46.0
[11] withr_2.1.2 colorspace_1.4-1 GOSemSim_2.10.0 Biobase_2.44.0 phyloseq_1.28.0
[16] rstudioapi_0.10 leaps_3.1 stats4_3.6.1 DOSE_3.10.2 urltools_1.7.3
[21] GenomeInfoDbData_1.2.1 polyclip_1.10-0 bit64_0.9-7 farver_2.0.3 rhdf5_2.28.1
[26] vctrs_0.2.2 generics_0.0.2 xfun_0.11 R6_2.4.1 GenomeInfoDb_1.20.0
[31] clue_0.3-57 illuminaio_0.26.0 graphlayouts_0.5.0 locfit_1.5-9.1 bitops_1.0-6
[36] microbiome_1.6.0 reshape_0.8.8 fgsea_1.10.1 gridGraphics_0.4-1 DelayedArray_0.10.0
[41] assertthat_0.2.1 scales_1.1.0 nnet_7.3-12 ggraph_2.0.0 enrichplot_1.4.0
[46] gtable_0.3.0 tidygraph_1.1.2 rlang_0.4.4 scatterplot3d_0.3-41 splines_3.6.1
[51] rtracklayer_1.44.4 acepack_1.4.1 GEOquery_2.52.0 checkmate_1.9.4 broom_0.5.3
[56] europepmc_0.3 BiocManager_1.30.10 reshape2_1.4.3 GenomicFeatures_1.36.4 backports_1.1.5
[61] Hmisc_4.3-0 clusterProfiler_3.12.0 tools_3.6.1 ggplotify_0.0.4 nor1mix_1.3-0
[66] biomformat_1.12.0 RColorBrewer_1.1-2 BiocGenerics_0.30.0 siggenes_1.58.0 ggridges_0.5.1
[71] Rcpp_1.0.3 plyr_1.8.5 base64enc_0.1-3 progress_1.2.2 zlibbioc_1.30.0
[76] purrr_0.3.3 RCurl_1.95-4.12 prettyunits_1.1.1 rpart_4.1-15 openssl_1.4.1
[81] viridis_0.5.1 cowplot_1.0.0 bumphunter_1.26.0 S4Vectors_0.22.1 SummarizedExperiment_1.14.1 [86] ggrepel_0.8.1 cluster_2.1.0 factoextra_1.0.6 magrittr_1.5 data.table_1.12.8
[91] DO.db_2.9 triebeard_0.3.0 matrixStats_0.55.0 hms_0.5.3 xtable_1.8-4
[96] XML_3.98-1.20 jpeg_0.1-8.1 mclust_5.4.5 IRanges_2.18.3 gridExtra_2.3
[101] compiler_3.6.1 biomaRt_2.40.5 minfi_1.30.0 tibble_2.1.3 crayon_1.3.4
[106] htmltools_0.4.0 Formula_1.2-3 geneplotter_1.62.0 tidyr_1.0.2 DBI_1.1.0
[111] tweenr_1.0.1 corrplot_0.84 ade4_1.7-13 readr_1.3.1 permute_0.9-5
[116] quadprog_1.5-8 igraph_1.2.4.2 GenomicRanges_1.36.1 pkgconfig_2.0.3 flashClust_1.01-2
[121] rvcheck_0.1.7 GenomicAlignments_1.20.1 registry_0.5-1 foreign_0.8-72 xml2_1.2.2
[126] foreach_1.4.8 annotate_1.62.0 rngtools_1.5 pkgmaker_0.31 multtest_2.40.0
[131] beanplot_1.2 XVector_0.24.0 bibtex_0.4.2.2 doRNG_1.7.1 scrime_1.3.5
[136] stringr_1.4.0 digest_0.6.24 vegan_2.5-6 Biostrings_2.52.0 base64_2.0
[141] fastmatch_1.1-0 htmlTable_1.13.3 edgeR_3.26.8 DelayedMatrixStats_1.6.1 Rsamtools_2.0.3
[146] lifecycle_0.1.0 jsonlite_1.6 Rhdf5lib_1.6.3 viridisLite_0.3.0 askpass_1.1
[151] pillar_1.4.3 lattice_0.20-38 httr_1.4.1 GO.db_3.8.2 glue_1.3.1
[156] UpSetR_1.4.0 png_0.1-7 iterators_1.0.12 bit_1.1-14 ggforce_0.3.1
[161] stringi_1.4.5 HDF5Array_1.12.3 blob_1.2.0 DESeq2_1.24.0 latticeExtra_0.6-29
[166] memoise_1.1.0 dplyr_0.8.3 ape_5.3 |