Question: SPIA function error in ToPASeq
0
gravatar for fawazfebin
17 months ago by
fawazfebin30
fawazfebin30 wrote:

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.

 

spia R pathway analysis topaseq • 297 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by fawazfebin30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 198 users visited in the last hour