Question: ELMER Package Error
0
gravatar for David_emir
2.6 years ago by
David_emir370
India
David_emir370 wrote:

Hello All, I am trying to work on DME and DGE analysis with TCGA data using ELMER package. but during creating for "createMAE: Construct a Multi-Assay Experiment for ELMER analysis" (The code is below) its showing an error as follows,

> mae <- createMAE(exp = exp, 
> +                  met = met,
> +                  save = TRUE,
> +                  linearize.exp = TRUE,
> +                  filter.probes = distal.probes,
> +                  save.filename = "mae_bioc2017.rda",
> +                  met.platform = "450K",
> +                  genome = "hg38",
> +                  TCGA = TRUE)

***Error in createMAE(exp = exp, met = met, save = TRUE, linearize.exp = TRUE,  : 
  could not find function "createMAE"***

Please let me know where i am missing, i have loaded all the necessary packages but it failed to recognize the basic ELMER function. Plese, i need your expert advice on this.

Thanks in Advance,

Sincerely, Dave,

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] TCGAbiolinks_2.7.21                               
 [2] devtools_1.13.5                                   
 [3] ELMER_1.6.0                                       
 [4] ELMER.data_1.6.0                                  
 [5] DT_0.4                                            
 [6] MultiAssayExperiment_1.2.1                        
 [7] data.table_1.10.4-3                               
 [8] BiocInstaller_1.26.1                              
 [9] Homo.sapiens_1.3.1                                
[10] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2           
[11] org.Hs.eg.db_3.4.1                                
[12] GO.db_3.4.1                                       
[13] OrganismDbi_1.18.1                                
[14] GenomicFeatures_1.28.5                            
[15] AnnotationDbi_1.38.2                              
[16] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[17] minfi_1.22.1                                      
[18] bumphunter_1.16.0                                 
[19] locfit_1.5-9.1                                    
[20] iterators_1.0.9                                   
[21] foreach_1.4.4                                     
[22] Biostrings_2.44.2                                 
[23] XVector_0.16.0                                    
[24] GlobalOptions_0.0.12                              
[25] jsonlite_1.5                                      
[26] httr_1.3.1                                        
[27] NMF_0.23.6                                        
[28] bigmemory_4.5.33                                  
[29] cluster_2.0.6                                     
[30] rngtools_1.2.4                                    
[31] pkgmaker_0.26.9                                   
[32] registry_0.5                                      
[33] ggplot2_2.2.1                                     
[34] dplyr_0.7.4                                       
[35] readr_1.1.1                                       
[36] DESeq2_1.16.1                                     
[37] SummarizedExperiment_1.6.5                        
[38] DelayedArray_0.2.7                                
[39] matrixStats_0.53.0                                
[40] Biobase_2.36.2                                    
[41] GenomicRanges_1.28.6                              
[42] GenomeInfoDb_1.12.3                               
[43] IRanges_2.10.5                                    
[44] S4Vectors_0.14.7                                  
[45] BiocGenerics_0.22.1                               
[46] magrittr_1.5                                      

loaded via a namespace (and not attached):
  [1] shinydashboard_0.6.1        R.utils_2.6.0              
  [3] RSQLite_2.0                 htmlwidgets_1.0            
  [5] grid_3.4.3                  trimcluster_0.1-2          
  [7] BiocParallel_1.10.1         DESeq_1.28.0               
  [9] munsell_0.4.3               codetools_0.2-15           
 [11] preprocessCore_1.38.1       withr_2.1.1                
 [13] colorspace_1.3-2            knitr_1.20                 
 [15] rstudioapi_0.7              robustbase_0.92-8          
 [17] git2r_0.19.0                GenomeInfoDbData_0.99.0    
 [19] mnormt_1.5-5                hwriter_1.3.2              
 [21] KMsurv_0.1-5                bit64_0.9-7                
 [23] downloader_0.4              ggthemes_3.4.0             
 [25] EDASeq_2.10.0               diptest_0.75-7             
 [27] R6_2.2.2                    doParallel_1.0.11          
 [29] illuminaio_0.18.0           flexmix_2.3-14             
 [31] bitops_1.0-6                reshape_0.8.7              
 [33] assertthat_0.2.0            scales_0.5.0               
 [35] nnet_7.3-12                 gtable_0.2.0               
 [37] sva_3.24.4                  rlang_0.2.0                
 [39] genefilter_1.58.1           cmprsk_2.2-7               
 [41] splines_3.4.3               rtracklayer_1.36.6         
 [43] lazyeval_0.2.1              acepack_1.4.1              
 [45] GEOquery_2.42.0             selectr_0.3-1              
 [47] broom_0.4.3                 checkmate_1.8.5            
 [49] yaml_2.1.16                 reshape2_1.4.3             
 [51] backports_1.1.2             httpuv_1.3.5               
 [53] Hmisc_4.1-1                 RBGL_1.52.0                
 [55] tools_3.4.3                 psych_1.7.8                
 [57] gridBase_0.4-7              nor1mix_1.2-3              
 [59] RColorBrewer_1.1-2          siggenes_1.50.0            
 [61] Rcpp_0.12.15                plyr_1.8.4                 
 [63] base64enc_0.1-3             progress_1.1.2             
 [65] zlibbioc_1.22.0             purrr_0.2.4                
 [67] RCurl_1.95-4.10             prettyunits_1.0.2          
 [69] ggpubr_0.1.6                rpart_4.1-11               
 [71] openssl_1.0                 GetoptLong_0.1.6           
 [73] viridis_0.5.0               zoo_1.8-1                  
 [75] ggrepel_0.7.0               circlize_0.4.3             
 [77] survminer_0.4.2             mvtnorm_1.0-7              
 [79] whisker_0.3-2               aroma.light_3.6.0          
 [81] mime_0.5                    hms_0.4.1                  
 [83] xtable_1.8-2                XML_3.98-1.9               
 [85] mclust_5.4                  gridExtra_2.3              
 [87] shape_1.4.3                 compiler_3.4.3             
 [89] biomaRt_2.35.11             tibble_1.4.2               
 [91] R.oo_1.21.0                 htmltools_0.3.6            
 [93] mgcv_1.8-22                 Formula_1.2-2              
 [95] tidyr_0.8.0                 geneplotter_1.54.0         
 [97] DBI_0.7                     matlab_1.0.2               
 [99] ComplexHeatmap_1.14.0       MASS_7.3-47                
[101] fpc_2.1-11                  ShortRead_1.34.2           
[103] Matrix_1.2-12               quadprog_1.5-5             
[105] R.methodsS3_1.7.1           bindr_0.1                  
[107] pkgconfig_2.0.1             km.ci_0.5-2                
[109] bigmemory.sri_0.1.3         GenomicAlignments_1.12.2   
[111] foreign_0.8-69              xml2_1.2.0                 
[113] annotate_1.54.0             multtest_2.32.0            
[115] beanplot_1.2                rvest_0.3.2                
[117] doRNG_1.6.6                 stringr_1.2.0              
[119] digest_0.6.15               ConsensusClusterPlus_1.40.0
[121] graph_1.54.0                base64_2.0                 
[123] survMisc_0.5.4              htmlTable_1.11.2           
[125] dendextend_1.6.0            edgeR_3.18.1               
[127] curl_3.1                    kernlab_0.9-25             
[129] shiny_1.0.5                 Rsamtools_1.28.0           
[131] modeltools_0.2-21           rjson_0.2.15               
[133] nlme_3.1-131                bindrcpp_0.2               
[135] viridisLite_0.3.0           limma_3.32.10              
[137] pillar_1.2.1                lattice_0.20-35            
[139] DEoptimR_1.0-8              survival_2.41-3            
[141] glue_1.2.0                  UpSetR_1.3.3               
[143] prabclus_2.2-6              bit_1.1-12                 
[145] class_7.3-14                stringi_1.1.6              
[147] blob_1.1.0                  latticeExtra_0.6-28        
[149] memoise_1.1.0
dge rna-seq dme elemer package • 1.0k views
ADD COMMENTlink modified 2.5 years ago by w2felixgeist0 • written 2.6 years ago by David_emir370

What happens if you try with ELMER::createMAE( )

ADD REPLYlink written 2.6 years ago by h.mon31k

Hi H. Mon, Thanks a lot for replying, I have tried using your code as well, its showing me the following error... Error: 'createMAE' is not an exported object from 'namespace:ELMER'

ADD REPLYlink written 2.6 years ago by David_emir370

Do your code really is:

> mae <- createMAE(exp = exp, 
> +                  met = met,

Because it should be:

mae <- createMAE(exp = exp, 
                  met = met,

Without the > and +.

ADD REPLYlink written 2.6 years ago by h.mon31k

Hi h.mon, When i copy from console to this site it created + and >. Actually my code is as follows, this throws error.

mae <- ELMER::createMAE(exp = exp, 
                 met = met,
                 save = TRUE,
                 linearize.exp = TRUE,
                 filter.probes = distal.probes,
                 save.filename = "mae_bioc2017.rda",
                 met.platform = "450K",
                 genome = "hg38",
                 TCGA = TRUE)
ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by David_emir370

Ok, I know this is rudimentary, but did you try closing R (and maybe RStudio, if you are using it), opening again and then try to run the analysis again?

ADD REPLYlink written 2.6 years ago by h.mon31k

I have tried that too, infact i had restarted my system twice but still it's shows same error.

ADD REPLYlink written 2.6 years ago by David_emir370

My last shot at a simple solution is, if you are running under RStudio, to try ELMER with plain R - I once had problems with some packages on RStudio.

ADD REPLYlink written 2.6 years ago by h.mon31k

Hi H.Mon, Have tried that as well ... It is still the same :( I am feeling so helpless now...

ADD REPLYlink written 2.6 years ago by David_emir370
0
gravatar for w2felixgeist
2.5 years ago by
w2felixgeist0 wrote:

Hi, I just had the same problem. There is no createMAE function in the binary package. You need to install it from source, then it works :)

ADD COMMENTlink written 2.5 years ago by w2felixgeist0
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