I just recently performed an upgrade of my R libraries, including upgrading my developmental BioConductor libraries.  After the upgrade, DEXSeq is giving me an error when I try to access the main dxd object that I have stored in .RData from prior sessions. In my case, I have named this object "dxd".

the simple command:

> str(dxd) 
Error in nrow(x@elementMetadata) :
  error in evaluating the argument 'x' in selecting a method for function 'nrow': Error: no slot of name "elementMetadata" for this object of class "DEXSeqDataSet"

Any thoughts?  Here is my sessionInfo

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

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=en_US.UTF-8
 [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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] DEXSeq_1.15.10             DESeq2_1.9.26
 [3] RcppArmadillo_0.5.400.2.0  Rcpp_0.12.0
 [5] SummarizedExperiment_0.3.2 GenomicRanges_1.21.17
 [7] GenomeInfoDb_1.5.9         IRanges_2.3.17
 [9] S4Vectors_0.7.12           Biobase_2.29.1
[11] BiocGenerics_0.15.5        BiocParallel_1.3.48

loaded via a namespace (and not attached):
 [1] genefilter_1.51.0     statmod_1.4.21        locfit_1.5-9.1
 [4] reshape2_1.4.1        splines_3.2.0         lattice_0.20-33
 [7] colorspace_1.2-6      survival_2.38-3       XML_3.98-1.1
[10] foreign_0.8-65        DBI_0.3.1             RColorBrewer_1.1-2
[13] lambda.r_1.1.7        plyr_1.8.3            stringr_1.0.0
[16] zlibbioc_1.15.0       Biostrings_2.37.3     munsell_0.4.2
[19] gtable_0.1.2          futile.logger_1.4.1   hwriter_1.3.2
[22] latticeExtra_0.6-26   geneplotter_1.47.0    biomaRt_2.25.1
[25] AnnotationDbi_1.31.17 proto_0.3-10          acepack_1.3-3.3
[28] xtable_1.7-4          scales_0.2.5          Hmisc_3.16-0
[31] annotate_1.47.4       XVector_0.9.1         Rsamtools_1.21.14
[34] gridExtra_2.0.0       ggplot2_1.0.1         digest_0.6.8
[37] stringi_0.5-5         grid_3.2.0            tools_3.2.0
[40] bitops_1.0-6          magrittr_1.5          RCurl_1.95-4.7
[43] RSQLite_1.0.0         Formula_1.2-1         cluster_2.0.3
[46] futile.options_1.0.0  MASS_7.3-43           rpart_4.1-10
[49] nnet_7.3-10

Hi Craig,

The internal representation of the DESeqDataSet class (which the DEXSeqDataSet class extends) has changed in BioC 3.2 (current devel). So any DESeqDataSet object (or derived) that was serialized (i.e. saved to an .RData file) using a prior version of BioC will look "broken" when loaded in BioC >= 3.2. To "fix" the object, just do:

library(DEXSeq)
dxd <- updateObject(dxd)

Cheers,

H.