Dear all, I analyzed RNA-seq data using DESeq2 extracting the results with or without shrinkage

without shrinkage:

res21 <- results(dds2, contrast=c("combined", "XX.DMSO", "XX.dTAG"),
                         cooksCutoff=FALSE, alpha=0.05)

with shrinkage:

resLFC1 <- lfcShrink(dds2, contrast=c("combined", "XX.DMSO", "XX.dTAG"),
                     alpha=0.05, type="ashr")

There is a small number of genes were the padj get's NA when including shrinking. Here is a table of the mentioned genes: https://drive.google.com/file/d/1RaHSHuDwtDiUT9-IDmmt3wp-0ImLuY2R/view

Why? Thank's for your help. Best Dagmar

sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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  methods   base     

other attached packages:
 [1] data.table_1.12.0          reshape2_1.4.3             BiocParallel_1.12.0        edgeR_3.20.9               limma_3.34.9              
 [6] hwriter_1.3.2              ReportingTools_2.17.3      knitr_1.21                 genefilter_1.60.0          org.Hs.eg.db_3.5.0        
[11] AnnotationDbi_1.40.0       ggplot2_3.1.0              PoiClaClu_1.0.2.1          RColorBrewer_1.1-2         pheatmap_1.0.12           
[16] DESeq2_1.18.1              SummarizedExperiment_1.8.1 DelayedArray_0.4.1         matrixStats_0.54.0         Biobase_2.38.0            
[21] GenomicRanges_1.30.3       GenomeInfoDb_1.14.0        IRanges_2.12.0             S4Vectors_0.16.0           BiocGenerics_0.24.0       
[26] Rsubread_1.28.1           

loaded via a namespace (and not attached):
  [1] backports_1.1.3               GOstats_2.44.0                Hmisc_4.2-0                   AnnotationHub_2.10.1         
  [5] plyr_1.8.4                    lazyeval_0.2.1                GSEABase_1.40.1               splines_3.4.4                
  [9] digest_0.6.18                 invgamma_1.1                  BiocInstaller_1.28.0          ensembldb_2.2.2              
 [13] htmltools_0.3.6               GO.db_3.5.0                   SQUAREM_2020.3                magrittr_1.5                 
 [17] checkmate_1.9.1               memoise_1.1.0                 BSgenome_1.46.0               cluster_2.0.7-1              
 [21] Biostrings_2.46.0             annotate_1.56.2               R.utils_2.8.0                 ggbio_1.26.1                 
 [25] prettyunits_1.0.2             colorspace_1.4-0              blob_1.1.1                    xfun_0.4                     
 [29] dplyr_0.8.0.1                 crayon_1.3.4                  RCurl_1.95-4.11               graph_1.56.0                 
 [33] survival_2.43-3               VariantAnnotation_1.24.5      glue_1.3.0                    gtable_0.2.0                 
 [37] zlibbioc_1.24.0               XVector_0.18.0                Rgraphviz_2.22.0              scales_1.1.1                 
 [41] DBI_1.0.0                     GGally_1.4.0                  Rcpp_1.0.4.6                  xtable_1.8-3                 
 [45] progress_1.2.0                htmlTable_1.13.1              foreign_0.8-71                bit_1.1-14                   
 [49] OrganismDbi_1.20.0            Formula_1.2-3                 AnnotationForge_1.20.0        truncnorm_1.0-8              
 [53] htmlwidgets_1.3               httr_1.4.0                    acepack_1.4.1                 pkgconfig_2.0.2              
 [57] reshape_0.8.8                 XML_3.98-1.17                 R.methodsS3_1.7.1             farver_2.0.3                 
 [61] nnet_7.3-12                   locfit_1.5-9.1                tidyselect_0.2.5              labeling_0.3                 
 [65] rlang_0.4.6                   later_0.8.0                   munsell_0.5.0                 tools_3.4.4                  
 [69] RSQLite_2.1.1                 evaluate_0.13                 stringr_1.4.0                 yaml_2.2.0                   
 [73] bit64_0.9-7                   purrr_0.3.0                   AnnotationFilter_1.2.0        RBGL_1.54.0                  
 [77] mime_0.6                      R.oo_1.22.0                   biomaRt_2.34.2                compiler_3.4.4               
 [81] rstudioapi_0.9.0              curl_3.3                      interactiveDisplayBase_1.16.0 PFAM.db_3.5.0                
 [85] tibble_2.0.1                  geneplotter_1.56.0            stringi_1.3.1                 highr_0.7                    
 [89] GenomicFeatures_1.30.3        lattice_0.20-38               ProtGenerics_1.10.0           Matrix_1.2-15                
 [93] pillar_1.3.1                  lifecycle_0.2.0               bitops_1.0-6                  irlba_2.3.3                  
 [97] httpuv_1.4.5.1                rtracklayer_1.38.3            R6_2.4.1                      latticeExtra_0.6-28          
[101] RMySQL_0.10.16                promises_1.0.1                gridExtra_2.3                 dichromat_2.0-0              
[105] assertthat_0.2.0              Category_2.44.0               withr_2.1.2                   GenomicAlignments_1.14.2     
[109] Rsamtools_1.30.0              GenomeInfoDbData_1.0.0        hms_0.4.2                     grid_3.4.4                   
[113] rpart_4.1-13                  ashr_2.2-47                   biovizBase_1.26.0             mixsqp_0.3-43                
[117] shiny_1.2.0                   base64enc_0.1-3

In the first command you turn off the cooksCutoff explicitely. In the second one, because you do not provide a res object the function calls results internally and by default cooksCutoff is TRUE for this. See the lfcShrink code for details and ?results for the defaults of results().