Question: too few significant regions by q-value using DER Finder
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gravatar for pourjam.cs
13 months ago by
pourjam.cs0
pourjam.cs0 wrote:

Hello. I have analysed 9 RNA-Seq samples from two sheep breeds' ovaries transcriptome using DER Finder package provided by Lieber institute. After setting arguments that are included in my R Code text, I gained too few differentially expressed regions (DER) passing the q-value cutoff of 0.1 and p-value of 0.05. Although, similar research on human brain transcriptome has been before conducted and high numbers of DERs were reported (50560), mine only 5 DERs been found. Some arguments passed to the function "analyzeChr" asre listed below. Permutation = 50 cuttoff = "theoretical" cuttoffFstat = 5e-2 annotationPackage = NULL

sessionInfo()

R version 3.5.3 (2019-03-11) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages: [1] TxDb.Oaries.BioMart.ENSEMBLMARTENSEMBL.Oarv3.1_3.5 rmarkdown_1.13 RMariaDB_1.0.6 ggbio_1.30.0
[5] org.Oaries.eg.db_0.1 AnnotationForge_1.24.0 GOstats_2.48.0 graph_1.60.0
[9] Category_2.48.1 Matrix_1.2-17 ensembldb_2.6.8 AnnotationFilter_1.6.0
[13] limma_3.38.3 knitr_1.23 forcats_0.4.0 stringr_1.4.0
[17] readr_1.3.1 tibble_2.1.3 tidyverse_1.2.1 biovizBase_1.30.1
[21] regionReport_1.16.1 curl_3.3 xml2_1.2.0 biomaRt_2.38.0
[25] AnnotationHub_2.14.5 usethis_1.5.0 devtools_2.0.2 RMySQL_0.10.17
[29] DBI_1.0.0 tidyr_0.8.3 derfinderPlot_1.16.1 ggplot2_3.1.1
[33] purrr_0.3.2 dplyr_0.8.1 rtracklayer_1.42.2 RSQLite_2.1.1
[37] GenomicFeatures_1.34.8 AnnotationDbi_1.44.0 GenomeInfoDbData_1.2.0 bumphunter_1.24.5
[41] locfit_1.5-9.1 iterators_1.0.10 foreach_1.4.4 DESeq2_1.22.2
[45] EDASeq_2.16.3 ShortRead_1.40.0 GenomicAlignments_1.18.1 SummarizedExperiment_1.12.0
[49] DelayedArray_0.8.0 matrixStats_0.54.0 Rsamtools_1.34.1 Biostrings_2.50.2
[53] XVector_0.22.0 BiocParallel_1.16.6 Biobase_2.42.0 GenomicRanges_1.34.0
[57] GenomeInfoDb_1.18.2 IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0
[61] derfinderData_2.0.0 derfinder_1.16.1

loaded via a namespace (and not attached): [1] R.utils_2.9.0 tidyselect_0.2.5 htmlwidgets_1.3 grid_3.5.3 DESeq_1.34.1 munsell_0.5.0 codetools_0.2-16
[8] withr_2.1.2 colorspace_1.4-1 OrganismDbi_1.24.0 rstudioapi_0.10 hwriter_1.3.2 bit64_0.9-7 rprojroot_1.3-2
[15] generics_0.0.2 xfun_0.7 markdown_1.0 R6_2.4.0 bitops_1.0-6 reshape_0.8.8 assertthat_0.2.1
[22] promises_1.0.1 scales_1.0.0 nnet_7.3-12 gtable_0.3.0 processx_3.3.1 rlang_0.3.4 genefilter_1.64.0
[29] splines_3.5.3 lazyeval_0.2.2 acepack_1.4.1 dichromat_2.0-0 broom_0.5.2 checkmate_1.9.3 modelr_0.1.4
[36] BiocManager_1.30.4 yaml_2.2.0 reshape2_1.4.3 backports_1.1.4 httpuv_1.5.1 qvalue_2.14.1 Hmisc_4.2-0
[43] RBGL_1.58.2 tools_3.5.3 RColorBrewer_1.1-2 sessioninfo_1.1.1 Rcpp_1.0.1 plyr_1.8.4 base64enc_0.1-3
[50] progress_1.2.2 zlibbioc_1.28.0 RCurl_1.95-4.12 ps_1.3.0 prettyunits_1.0.2 rpart_4.1-15 GenomicFiles_1.18.0
[57] haven_2.1.0 cluster_2.0.9 fs_1.3.1 magrittr_1.5 data.table_1.12.2 ProtGenerics_1.14.0 pkgload_1.0.2
[64] aroma.light_3.12.0 hms_0.4.2 mime_0.7 evaluate_0.14 xtable_1.8-4 XML_3.98-1.20 readxl_1.3.1
[71] gridExtra_2.3 testthat_2.1.1 compiler_3.5.3 crayon_1.3.4 R.oo_1.22.0 htmltools_0.3.6 later_0.8.0
[78] Formula_1.2-3 geneplotter_1.60.0 lubridate_1.7.4 BiocStyle_2.10.0 cli_1.1.0 R.methodsS3_1.7.1 derfinderHelper_1.16.1
[85] pkgconfig_2.0.2 registry_0.5-1 RefManageR_1.2.12 foreign_0.8-71 annotate_1.60.1 rngtools_1.3.1 DEFormats_1.10.1
[92] pkgmaker_0.27 rvest_0.3.4 bibtex_0.4.2 knitcitations_1.0.8 doRNG_1.7.1 VariantAnnotation_1.28.13 callr_3.2.0
[99] digest_0.6.19 cellranger_1.1.0 htmlTable_1.13.1 edgeR_3.24.3 GSEABase_1.44.0 shiny_1.3.2 knitrBootstrap_1.0.2
[106] nlme_3.1-140 jsonlite_1.6 desc_1.2.0 BSgenome_1.50.0 pillar_1.4.1 lattice_0.20-38 GGally_1.4.0
[113] GO.db_3.7.0 httr_1.4.0 pkgbuild_1.0.3 survival_2.44-1.1 interactiveDisplayBase_1.20.0 glue_1.3.1 remotes_2.0.4
[120] Rgraphviz_2.26.0 bit_1.1-14 stringi_1.4.3 blob_1.1.1 latticeExtra_0.6-28 memoise_1.1.0

rna-seq R • 262 views
ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 13 months ago by pourjam.cs0
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