Entering edit mode
fawazfebin
▴
60
@fawazfebin-14053
Last seen 4.3 years ago
Hi
I was doing a pathway analysis of RNA-Seq data using ToPASeq program. I ran the following commands :
> library("ToPASeq") > library("gageData") > DEXcounts = read.table("/home/febin/DEXcounts.txt", header = TRUE ,row.names = 1) > DEXcounts = DEXcounts[,6:ncol(DEXcounts)] > DEXcounts <- DEXcounts[rowSums(DEXcounts)>0,] > grpTopDex = c(rep("cntrl",2),rep("dex2",2),rep("dex4",2)) > kegg<-pathways("hsapiens","kegg") > spi<-SPIA(DEXcounts, grpTopDex, kegg,type="RNASeq") Error in .local(object, which, ...) : unused argument (stringsAsFactors = FALSE)
Here is my sessionInfo
> sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 [4] LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8 [7] LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] gageData_2.16.0 ToPASeq_1.11.0 Rgraphviz_2.22.0 locfit_1.5-9.1 graph_1.56.0 [6] BiocGenerics_0.24.0 gRbase_1.8-3 graphite_1.24.1 edgeR_3.20.9 limma_3.34.9 loaded via a namespace (and not attached): [1] bitops_1.0-6 matrixStats_0.53.1 bit64_0.9-7 [4] progress_1.1.2 doParallel_1.0.11 RColorBrewer_1.1-2 [7] httr_1.3.1 GenomeInfoDb_1.14.0 tools_3.4.3 [10] backports_1.1.2 R6_2.2.2 rpart_4.1-13 [13] Hmisc_4.1-1 DBI_0.8 lazyeval_0.2.1 [16] colorspace_1.3-2 nnet_7.3-12 prettyunits_1.0.2 [19] RMySQL_0.10.14 gridExtra_2.3 DESeq2_1.18.1 [22] bit_1.1-12 compiler_3.4.3 clipper_1.18.0 [25] Biobase_2.38.0 htmlTable_1.11.2 DelayedArray_0.4.1 [28] rtracklayer_1.38.3 KEGGgraph_1.38.0 scales_0.5.0 [31] checkmate_1.8.5 mvtnorm_1.0-7 qpgraph_2.12.0 [34] genefilter_1.60.0 RBGL_1.54.0 rappdirs_0.3.1 [37] DESeq_1.30.0 Rsamtools_1.30.0 stringr_1.3.0 [40] digest_0.6.15 foreign_0.8-69 R.utils_2.6.0 [43] XVector_0.18.0 base64enc_0.1-3 pkgconfig_2.0.1 [46] htmltools_0.3.6 maps_3.2.0 htmlwidgets_1.0 [49] rlang_0.2.0 rstudioapi_0.7 RSQLite_2.0 [52] BiocParallel_1.12.0 acepack_1.4.1 R.oo_1.21.0 [55] RCurl_1.95-4.10 magrittr_1.5 qtl_1.42-8 [58] GenomeInfoDbData_1.0.0 Formula_1.2-2 dotCall64_0.9-5.2 [61] Matrix_1.2-11 Rcpp_0.12.16 munsell_0.4.3 [64] S4Vectors_0.16.0 R.methodsS3_1.7.1 stringi_1.1.7 [67] yaml_2.1.18 SummarizedExperiment_1.8.1 zlibbioc_1.24.0 [70] plyr_1.8.4 blob_1.1.1 lattice_0.20-35 [73] Biostrings_2.46.0 splines_3.4.3 GenomicFeatures_1.30.3 [76] annotate_1.56.2 knitr_1.20 pillar_1.2.1 [79] igraph_1.2.1 GenomicRanges_1.30.3 corpcor_1.6.9 [82] biomaRt_2.34.2 codetools_0.2-15 geneplotter_1.56.0 [85] stats4_3.4.3 XML_3.98-1.10 latticeExtra_0.6-28 [88] data.table_1.10.4-3 spam_2.1-3 foreach_1.4.4 [91] gtable_0.2.0 assertthat_0.2.0 ggplot2_2.2.1 [94] TeachingDemos_2.10 xtable_1.8-2 survival_2.41-3 [97] tibble_1.4.2 iterators_1.0.9 GenomicAlignments_1.14.1 [100] AnnotationDbi_1.40.0 memoise_1.1.0 IRanges_2.12.0 [103] fields_9.6 cluster_2.0.6
How can I overcome this error? Thanks in advance.