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I'm running a Deseq2 with RNA seq data to compare between test and control which every condition has 3 duplicated. But when I compare between test vs. control I got 1797 DEG but control against test I got 1760 genes.
res<-results(dds, contrast = c("dex", "T0", "T20"),alpha = 0.05)
res2 <- lfcShrink(dds=dds, coef="dex_T0_vs_T20")
sig <- res2[ which(res2$padj < 0.05), ]
summary(sig)
out of 1797 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up) : 952, 53%
LFC < 0 (down) : 845, 47%
res<-results(dds, contrast = c("dex", "T20", "T0"),alpha = 0.05)
res2 <- lfcShrink(dds=dds, coef="dex_T20_vs_T0")
sig <- res2[ which(res2$padj < 0.05), ]
summary(sig)
out of 1760 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 929, 53%
LFC < 0 (down) : 831, 47%
sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Thai_Thailand.874 LC_CTYPE=Thai_Thailand.874
[3] LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C
[5] LC_TIME=Thai_Thailand.874
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] RColorBrewer_1.1-2 Biostrings_2.56.0
[3] XVector_0.28.0 stringr_1.4.0
[5] dplyr_1.0.2 DESeq2_1.28.1
[7] SummarizedExperiment_1.18.2 DelayedArray_0.14.1
[9] matrixStats_0.57.0 Biobase_2.48.0
[11] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
[13] IRanges_2.22.2 S4Vectors_0.26.1
[15] BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] bdsmatrix_1.3-4 Rcpp_1.0.5 locfit_1.5-9.4
[4] mvtnorm_1.1-1 apeglm_1.10.0 lattice_0.20-41
[7] digest_0.6.25 plyr_1.8.6 R6_2.4.1
[10] emdbook_1.3.12 coda_0.19-4 RSQLite_2.2.1
[13] ggplot2_3.3.2 pillar_1.4.6 zlibbioc_1.34.0
[16] rlang_0.4.7 rstudioapi_0.11 annotate_1.66.0
[19] blob_1.2.1 Matrix_1.2-18 bbmle_1.0.23.1
[22] splines_4.0.2 BiocParallel_1.22.0 geneplotter_1.66.0
[25] RCurl_1.98-1.2 bit_4.0.4 munsell_0.5.0
[28] tinytex_0.26 numDeriv_2016.8-1.1 compiler_4.0.2
[31] xfun_0.18 pkgconfig_2.0.3 tidyselect_1.1.0
[34] tibble_3.0.3 GenomeInfoDbData_1.2.3 XML_3.99-0.5
[37] crayon_1.3.4 MASS_7.3-51.6 bitops_1.0-6
[40] grid_4.0.2 xtable_1.8-4 gtable_0.3.0
[43] lifecycle_0.2.0 DBI_1.1.0 magrittr_1.5
[46] scales_1.1.1 stringi_1.5.3 genefilter_1.70.0
[49] ellipsis_0.3.1 vctrs_0.3.4 generics_0.0.2
[52] tools_4.0.2 bit64_4.0.5 glue_1.4.2
[55] purrr_0.3.4 survival_3.1-12 AnnotationDbi_1.50.3
[58] colorspace_1.4-1 memoise_1.1.0