某个 DESeq2 版本可分析无重复但极为严格

分析结果

[1] "OE11_24h" "OE11_3h"
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
using 'apeglm' for LFC shrinkage. If used in published research, please cite:
Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
sequence count data: removing the noise and preserving large differences.
bioRxiv. https://doi.org/10.1101/303255

out of 21015 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 0, 0%
LFC < 0 (down) : 0, 0%
outliers [1] : 0, 0%
low counts [2] : 0, 0%
(mean count < 5)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results
[1] 0

工作台信息

R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/chengjie_chen/anaconda3/envs/DiffExp/lib/R/lib/libRblas.so

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

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

other attached packages:
[1] DESeq2_1.20.0 SummarizedExperiment_1.10.1
[3] DelayedArray_0.6.6 BiocParallel_1.14.2
[5] matrixStats_0.61.0 Biobase_2.40.0
[7] GenomicRanges_1.32.7 GenomeInfoDb_1.16.0
[9] IRanges_2.14.12 S4Vectors_0.18.3
[11] BiocGenerics_0.26.0

loaded via a namespace (and not attached):
[1] locfit_1.5-9.4 Rcpp_1.0.7 lattice_0.20-45
[4] digest_0.6.29 utf8_1.2.2 R6_2.5.1
[7] backports_1.4.1 acepack_1.4.0 RSQLite_2.2.9
[10] ggplot2_3.3.5 pillar_1.6.4 zlibbioc_1.26.0
[13] rlang_0.4.12 rstudioapi_0.13 data.table_1.14.2
[16] annotate_1.58.0 blob_1.2.2 rpart_4.1-15
[19] Matrix_1.4-0 checkmate_2.0.0 splines_3.5.1
[22] geneplotter_1.58.0 stringr_1.4.0 foreign_0.8-70
[25] htmlwidgets_1.5.4 bit_4.0.4 RCurl_1.98-1.5
[28] munsell_0.5.0 compiler_3.5.1 xfun_0.29
[31] pkgconfig_2.0.3 base64enc_0.1-3 htmltools_0.5.2
[34] nnet_7.3-16 tibble_3.1.6 gridExtra_2.3
[37] htmlTable_2.3.0 GenomeInfoDbData_1.1.0 Hmisc_4.1-1
[40] XML_3.99-0.3 fansi_0.5.0 crayon_1.4.2
[43] bitops_1.0-7 grid_3.5.1 DBI_1.1.2
[46] xtable_1.8-4 gtable_0.3.0 lifecycle_1.0.1
[49] magrittr_2.0.1 scales_1.1.1 cachem_1.0.6
[52] stringi_1.7.6 XVector_0.20.0 genefilter_1.62.0
[55] latticeExtra_0.6-28 ellipsis_0.3.2 vctrs_0.3.8
[58] Formula_1.2-4 RColorBrewer_1.1-2 tools_3.5.1
[61] bit64_4.0.5 glue_1.6.0 fastmap_1.1.0
[64] survival_3.2-13 AnnotationDbi_1.42.1 colorspace_2.0-2
[67] cluster_2.1.2 memoise_2.0.1 knitr_1.37