Hi Folks,

Thanks for deseq2. I think there might be a small bug in rlog where it doesn't copy rownames from the source matrix? The below shows str() for rlog and vst output (with the same count matrix input) respectively and the rlog has NULL rownames. In the vst code there is a specific rownames copy assignment but not in the rlog code. This causes problems when adding them directly as assays in a SummarizedExperiment as the rlog assay values become NA's.

 num [1:15442, 1:28] 4.88 3.66 6.82 5.29 6.84 ...
 - attr(*, "dimnames")=List of 2
  ..$ : NULL
  ..$ : chr [1:28] "G_tumor_KO_aPDL1_1" "G_tumor_KO_aPDL1_2" "G_tumor_KO_aPDL1_4" "G_tumor_KO_aPDL1_5" ...
 - attr(*, "betaPriorVar")= num 3.84
 - attr(*, "intercept")= num [1:15442, 1] 5.42 4.47 7.86 7 7.87 ...

 num [1:15442, 1:28] 5.89 5.26 6.95 5.84 6.97 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:15442] "ENSMUSG00000014198" "ENSMUSG00000048794" "ENSMUSG00000028020" "ENSMUSG00000042096" ...
  ..$ : chr [1:28] "G_tumor_KO_aPDL1_1" "G_tumor_KO_aPDL1_2" "G_tumor_KO_aPDL1_4" "G_tumor_KO_aPDL1_5" ...

Thanks,

Tim

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.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=C
 [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_1.24.0               shinyngs_0.0.1
 [3] SummarizedExperiment_1.14.1 DelayedArray_0.10.0
 [5] BiocParallel_1.18.1         matrixStats_0.55.0
 [7] Biobase_2.44.0              GenomicRanges_1.36.1
 [9] GenomeInfoDb_1.20.0         IRanges_2.18.3
[11] S4Vectors_0.22.1            BiocGenerics_0.30.0

loaded via a namespace (and not attached):
 [1] ggdendro_0.1-20        httr_1.4.1             tidyr_1.0.0
 [4] bit64_0.9-7            jsonlite_1.6           viridisLite_0.3.0
 [7] splines_3.6.1          Formula_1.2-3          shiny_1.4.0
[10] assertthat_0.2.1       latticeExtra_0.6-28    blob_1.2.0
[13] GenomeInfoDbData_1.2.1 yaml_2.2.0             RSQLite_2.1.2
[16] pillar_1.4.2           backports_1.1.5        lattice_0.20-38
[19] glue_1.3.1             digest_0.6.21          RColorBrewer_1.1-2
[22] promises_1.1.0         XVector_0.24.0         checkmate_1.9.4
[25] colorspace_1.4-1       htmltools_0.4.0        httpuv_1.5.2
[28] Matrix_1.2-17          plyr_1.8.4             XML_3.98-1.20
[31] pkgconfig_2.0.3        genefilter_1.66.0      zlibbioc_1.30.0
[34] purrr_0.3.2            xtable_1.8-4           scales_1.0.0
[37] later_1.0.0            annotate_1.62.0        tibble_2.1.3
[40] htmlTable_1.13.2       ggplot2_3.2.1          nnet_7.3-12
[43] lazyeval_0.2.2         survival_2.44-1.1      magrittr_1.5
[46] crayon_1.3.4           mime_0.7               memoise_1.1.0
[49] MASS_7.3-51.4          foreign_0.8-71         tools_3.6.1
[52] data.table_1.12.4      lifecycle_0.1.0        stringr_1.4.0
[55] plotly_4.9.0           locfit_1.5-9.1         munsell_0.5.0
[58] cluster_2.1.0          AnnotationDbi_1.46.1   compiler_3.6.1
[61] rlang_0.4.0            grid_3.6.1             RCurl_1.95-4.12
[64] rstudioapi_0.10        htmlwidgets_1.5.1      bitops_1.0-6
[67] base64enc_0.1-3        gtable_0.3.0           DBI_1.0.0
[70] R6_2.4.0               gridExtra_2.3          knitr_1.25
[73] dplyr_0.8.3            bit_1.1-14             fastmap_1.0.1
[76] zeallot_0.1.0          Hmisc_4.2-0            stringi_1.4.3
[79] Rcpp_1.0.2             geneplotter_1.62.0     vctrs_0.2.0
[82] rpart_4.1-15           acepack_1.4.1          tidyselect_0.2.5
[85] xfun_0.10
>

Can you post your code? Are you using rlog()?