Entering edit mode
The results(dds) function in DESeq2 gives Na values for padj, which I find quite puzzling. From what I understand, In principle, if the pval is there, the adjusted pval should not be NA. I checked the entire column of pvalue and there is no NA value.
As a Example,
res <- results(dds1)
head(res, 30)
The output is :
log2 fold change (MLE): condition Infected vs control
Wald test p-value: condition Infected vs control
DataFrame with 30 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
ENSMUSG00000102628 1.14237e-01 0.425855 5.143224 0.0827992 0.934011 NA
ENSMUSG00000100595 1.03784e+00 2.596535 2.155339 1.2046989 0.228320 NA
ENSMUSG00000097426 8.81255e-02 0.273996 5.143224 0.0532733 0.957514 NA
ENSMUSG00000104385 2.75549e-01 -1.871954 2.382787 -0.7856153 0.432093 NA
ENSMUSG00000102135 1.30991e+03 0.191029 0.158737 1.2034269 0.228811 0.543587
... ... ... ... ... ... ...
ENSMUSG00000090243 0.281665 -0.668478 2.563541 -0.260764 0.7942747 NA
ENSMUSG00000100701 0.720093 2.086543 4.345479 0.480164 0.6311107 NA
ENSMUSG00000100555 66.338703 -0.624417 0.359642 -1.736216 0.0825256 0.339681
ENSMUSG00000038702 53.606263 -0.185831 0.253518 -0.733010 0.4635526 0.738668
ENSMUSG00000101875 386.361469 0.304486 0.178201 1.708662 0.0875137 0.349655
In case you want to take a look at the entire results table , then here it is : https://github.com/MysoreSparrow/AZB_DataAnalysis/blob/main/results.csv.
sessionInfo( )
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
system code page: 65001
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] apeglm_1.16.0 BiocManager_1.30.16 glmpca_0.2.0
[4] genefilter_1.76.0 org.Mm.eg.db_3.14.0 AnnotationDbi_1.56.2
[7] gplots_3.1.3 EnhancedVolcano_1.12.0 ggrepel_0.9.1
[10] vsn_3.62.0 forcats_0.5.1 stringr_1.4.0
[13] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2
[16] tidyr_1.2.0 tibble_3.1.7 ggplot2_3.3.6
[19] tidyverse_1.3.1 RColorBrewer_1.1-3 pheatmap_1.0.12
[22] PoiClaClu_1.0.2.1 DESeq2_1.34.0 SummarizedExperiment_1.24.0
[25] Biobase_2.54.0 MatrixGenerics_1.6.0 matrixStats_0.62.0
[28] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0
[31] S4Vectors_0.32.4 BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] ggbeeswarm_0.6.0 colorspace_2.0-3 ellipsis_0.3.2 XVector_0.34.0
[5] fs_1.5.2 rstudioapi_0.13 farver_2.1.0 hexbin_1.28.2
[9] affyio_1.64.0 bit64_4.0.5 mvtnorm_1.1-3 fansi_1.0.3
[13] lubridate_1.8.0 xml2_1.3.3 splines_4.1.3 extrafont_0.18
[17] cachem_1.0.6 geneplotter_1.72.0 knitr_1.39 jsonlite_1.8.0
[21] Rttf2pt1_1.3.10 broom_0.8.0 annotate_1.72.0 dbplyr_2.1.1
[25] png_0.1-7 compiler_4.1.3 httr_1.4.3 backports_1.4.1
[29] assertthat_0.2.1 Matrix_1.4-0 fastmap_1.1.0 limma_3.50.3
[33] cli_3.2.0 htmltools_0.5.2 tools_4.1.3 coda_0.19-4
[37] gtable_0.3.0 glue_1.6.2 GenomeInfoDbData_1.2.7 affy_1.72.0
[41] maps_3.4.0 Rcpp_1.0.8.3 bbmle_1.0.25 cellranger_1.1.0
[45] vctrs_0.4.1 Biostrings_2.62.0 ggalt_0.4.0 preprocessCore_1.56.0
[49] extrafontdb_1.0 xfun_0.30 rvest_1.0.2 lifecycle_1.0.1
[53] gtools_3.9.2 XML_3.99-0.9 zlibbioc_1.40.0 MASS_7.3-55
[57] scales_1.2.0 ragg_1.2.2 hms_1.1.1 parallel_4.1.3
[61] proj4_1.0-11 yaml_2.3.5 memoise_2.0.1 ggrastr_1.0.1
[65] emdbook_1.3.12 bdsmatrix_1.3-4 stringi_1.7.6 RSQLite_2.2.14
[69] caTools_1.18.2 BiocParallel_1.28.3 systemfonts_1.0.4 rlang_1.0.2
[73] pkgconfig_2.0.3 bitops_1.0-7 evaluate_0.15 lattice_0.20-45
[77] labeling_0.4.2 bit_4.0.4 tidyselect_1.1.2 plyr_1.8.7
[81] magrittr_2.0.3 R6_2.5.1 generics_0.1.2 DelayedArray_0.20.0
[85] DBI_1.1.2 pillar_1.7.0 haven_2.5.0 withr_2.5.0
[89] survival_3.2-13 KEGGREST_1.34.0 RCurl_1.98-1.6 ash_1.0-15
[93] modelr_0.1.8 crayon_1.5.1 KernSmooth_2.23-20 utf8_1.2.2
[97] tzdb_0.3.0 rmarkdown_2.14 locfit_1.5-9.5 grid_4.1.3
[101] readxl_1.4.0 blob_1.2.3 reprex_2.0.1 digest_0.6.29
[105] xtable_1.8-4 numDeriv_2016.8-1.1 textshaping_0.3.6 munsell_0.5.0
[109] beeswarm_0.4.0 vipor_0.4.5
