ELMER Package Error
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
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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 :)
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What happens if you try with
ELMER::createMAE( )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'
Do your code really is:
Because it should be:
Without the
>and+.Hi h.mon, When i copy from console to this site it created + and >. Actually my code is as follows, this throws error.
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?
I have tried that too, infact i had restarted my system twice but still it's shows same error.
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.
Hi H.Mon, Have tried that as well ... It is still the same :( I am feeling so helpless now...