Dear DiffBind developers/users,

I have runned my histone ChIP-seq differential analysis using DiffBind some months ago. Back then I saved my output from dba.analyze(test_contrast, method=DBA_ALL_METHODS) as an .RDS file. At that point I also used DiffBind to make some Volcano plots and heatmaps. Now I wanted to change the colors of the heatmaps and I have loaded my .RDS file int R, but when I try to run dba.plotHeatmap i get an error:

Error in !pv$norm$DESeq2$bSubControl : invalid argument type

Does anyone know solution for this?

Thanks Maja

sessionInfo( )

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.8 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.15.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] remotes_2.4.2               qqman_0.1.8                 EnrichedHeatmap_1.24.0      ComplexHeatmap_2.10.0      
 [5] BiocParallel_1.28.3         forcats_0.5.2               stringr_1.5.0               purrr_0.3.4                
 [9] tibble_3.1.6                tidyverse_1.3.2             DiffBind_3.4.11             SummarizedExperiment_1.24.0
[13] MatrixGenerics_1.6.0        matrixStats_0.62.0          GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
[17] org.Mm.eg.db_3.14.0         AnnotationDbi_1.56.2        IRanges_2.28.0              S4Vectors_0.32.4           
[21] Biobase_2.54.0              BiocGenerics_0.40.0         clusterProfiler_4.2.2       BiocManager_1.30.18        
[25] ggplot2_3.3.6               enrichplot_1.14.2           writexl_1.4.0               tidyr_1.2.0                
[29] dplyr_1.0.9                 readxl_1.4.0                readr_2.1.2                

loaded via a namespace (and not attached):
  [1] utf8_1.2.3               tidyselect_1.2.0         RSQLite_2.2.14           htmlwidgets_1.6.2       
  [5] scatterpie_0.1.7         munsell_0.5.0            codetools_0.2-18         interp_1.1-3            
  [9] systemPipeR_2.0.8        withr_2.5.0              colorspace_2.1-0         GOSemSim_2.20.0         
 [13] rstudioapi_0.13          DOSE_3.20.1              labeling_0.4.2           bbmle_1.0.25            
 [17] GenomeInfoDbData_1.2.7   mixsqp_0.3-48            hwriter_1.3.2.1          polyclip_1.10-0         
 [21] bit64_4.0.5              farver_2.1.1             downloader_0.4           coda_0.19-4             
 [25] vctrs_0.4.1              treeio_1.18.1            generics_0.1.3           timechange_0.1.1        
 [29] R6_2.5.1                 doParallel_1.0.17        clue_0.3-64              apeglm_1.16.0           
 [33] graphlayouts_0.8.0       invgamma_1.1             locfit_1.5-9.6           bitops_1.0-7            
 [37] cachem_1.0.8             fgsea_1.20.0             gridGraphics_0.5-1       DelayedArray_0.20.0     
 [41] assertthat_0.2.1         vroom_1.5.7              BiocIO_1.4.0             scales_1.2.1            
 [45] ggraph_2.0.5             googlesheets4_1.0.1      gtable_0.3.0             tidygraph_1.2.1         
 [49] rlang_1.0.6              genefilter_1.76.0        calibrate_1.7.7          GlobalOptions_0.1.2     
 [53] splines_4.1.2            rtracklayer_1.54.0       lazyeval_0.2.2           gargle_1.2.1            
 [57] broom_1.0.2              yaml_2.3.7               reshape2_1.4.4           modelr_0.1.10           
 [61] backports_1.4.1          qvalue_2.26.0            tools_4.1.2              ggplotify_0.1.0         
 [65] ellipsis_0.3.2           gplots_3.1.3             RColorBrewer_1.1-3       Rcpp_1.0.10             
 [69] plyr_1.8.7               zlibbioc_1.40.0          RCurl_1.98-1.7           deldir_1.0-6            
 [73] GetoptLong_1.0.5         viridis_0.6.2            ashr_2.2-54              cluster_2.1.2           
 [77] haven_2.5.1              ggrepel_0.9.1            fs_1.6.2                 magrittr_2.0.3          
 [81] data.table_1.14.8        DO.db_2.9                circlize_0.4.15          reprex_2.0.2            
 [85] googledrive_2.0.0        truncnorm_1.0-8          mvtnorm_1.1-3            SQUAREM_2021.1          
 [89] amap_0.8-19              xtable_1.8-4             hms_1.1.1                patchwork_1.1.1         
 [93] XML_3.99-0.10            emdbook_1.3.12           jpeg_0.1-10              shape_1.4.6             
 [97] gridExtra_2.3            compiler_4.1.2           bdsmatrix_1.3-6          KernSmooth_2.23-20      
[101] crayon_1.5.2             shadowtext_0.1.2         htmltools_0.5.5          ggfun_0.0.6             
[105] tzdb_0.3.0               geneplotter_1.72.0       aplot_0.1.6              lubridate_1.9.0         
[109] DBI_1.1.3                tweenr_1.0.2             dbplyr_2.2.0             MASS_7.3-54             
[113] ShortRead_1.52.0         Matrix_1.3-4             cli_3.6.1                parallel_4.1.2          
[117] igraph_1.3.2             pkgconfig_2.0.3          GenomicAlignments_1.30.0 numDeriv_2016.8-1.1     
[121] xml2_1.3.4               foreach_1.5.2            annotate_1.72.0          ggtree_3.2.1            
[125] XVector_0.34.0           rvest_1.0.3              yulab.utils_0.0.4        digest_0.6.31           
[129] Biostrings_2.62.0        cellranger_1.1.0         fastmatch_1.1-3          tidytree_0.3.9          
[133] edgeR_3.36.0             restfulr_0.0.15          GreyListChIP_1.26.0      Rsamtools_2.10.0        
[137] gtools_3.9.2.2           rjson_0.2.21             lifecycle_1.0.3          nlme_3.1-153            
[141] jsonlite_1.8.4           viridisLite_0.4.2        limma_3.50.3             BSgenome_1.62.0         
[145] fansi_1.0.4              pillar_1.7.0             lattice_0.20-45          survival_3.2-13         
[149] KEGGREST_1.34.0          fastmap_1.1.1            httr_1.4.6               GO.db_3.14.0            
[153] glue_1.6.2               png_0.1-7                iterators_1.0.14         bit_4.0.4               
[157] ggforce_0.3.3            stringi_1.7.12           blob_1.2.3               DESeq2_1.34.0           
[161] latticeExtra_0.6-30      caTools_1.18.2           memoise_2.0.1            irlba_2.3.5.1           
[165] ape_5.6-2

You need to update to the current version of R and Bioconductor and then let us know if you still have problems. We cannot support old versions of R and Bioconductor.