DESeq2: invalid class “GRangesList” object

Question

[alesssia]

Hi all,

I am not sure if this is the right place to ask this question, but I've just updated my DESeq2 package from version 1.4.5 to version 1.6.3 and my scripts are no longer working. Specifically, I get the following error when generating a DESeqDataSet object with the function DESeqDataSetFromMatrix:

Error in validObject(.Object) :
invalid class "GRangesList" object: number of rows in DataTable 'mcols(x)' must match length of 'x'

To replicate this error one may either use the example shown in the DESeq2 vignette:

library("pasilla")
library("Biobase")
data("pasillaGenes")
countData <- counts(pasillaGenes)
colData <- pData(pasillaGenes)[,c("condition","type")]
dds <- DESeqDataSetFromMatrix(countData = countData,
                              colData = colData,
                              design = ~ condition)

or the example shown in the DESeq2 Reference Manual:

countData <- matrix(1:4,ncol=2)
colData <- data.frame(condition=factor(c("a","b")))
dds <- DESeqDataSetFromMatrix(countData, colData, formula(~ condition))

Thanks in advance for your help,
Alessia

sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

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] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] DESeq2_1.6.3            RcppArmadillo_0.4.400.0 Rcpp_0.11.2
[4] GenomicRanges_1.16.4    GenomeInfoDb_1.0.2      IRanges_1.22.10
[7] S4Vectors_0.4.0         BiocGenerics_0.12.1     BiocInstaller_1.16.1

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      annotate_1.42.1      AnnotationDbi_1.26.0
 [4] BatchJobs_1.3        BBmisc_1.7           Biobase_2.24.0
 [7] BiocParallel_0.6.1   brew_1.0-6           checkmate_1.4
[10] cluster_1.15.3       codetools_0.2-9      colorspace_1.2-4
[13] DBI_0.3.0            digest_0.6.4         fail_1.2
[16] foreach_1.4.2        foreign_0.8-61       Formula_1.1-2
[19] genefilter_1.46.1    geneplotter_1.42.0   ggplot2_1.0.0
[22] grid_3.1.0           gtable_0.1.2         Hmisc_3.14-5
[25] iterators_1.0.7      lattice_0.20-29      latticeExtra_0.6-26
[28] locfit_1.5-9.1       MASS_7.3-34          munsell_0.4.2
[31] nnet_7.3-8           plyr_1.8.1           proto_0.3-10
[34] RColorBrewer_1.0-5   reshape2_1.4         rpart_4.1-8
[37] RSQLite_0.11.4       scales_0.2.4         sendmailR_1.1-2
[40] splines_3.1.0        stringr_0.6.2        survival_2.37-7
[43] tools_3.1.0          XML_3.98-1.1         xtable_1.7-4
[46] XVector_0.4.0

Bioconductor version 3.0 (BiocInstaller 1.16.1)

[Devon Ryan]

I would guess that this is an incompatibility with the version of GenomicRanges you have. The problematic code works on my system:

R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

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] DESeq2_1.6.3              RcppArmadillo_0.4.650.1.1
 [3] Rcpp_0.11.4               GenomicRanges_1.18.4
 [5] GenomeInfoDb_1.2.4        IRanges_2.0.1
 [7] S4Vectors_0.4.0           pasilla_0.5.1
 [9] BiocInstaller_1.16.1      Biobase_2.26.0
[11] BiocGenerics_0.12.1

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      annotate_1.44.0      AnnotationDbi_1.28.1
 [4] base64enc_0.1-2      BatchJobs_1.5        BBmisc_1.9
 [7] BiocParallel_1.0.3   brew_1.0-6           checkmate_1.5.1
[10] cluster_2.0.1        codetools_0.2-10     colorspace_1.2-4
[13] DBI_0.3.1            digest_0.6.8         fail_1.2
[16] foreach_1.4.2        foreign_0.8-62       Formula_1.2-0
[19] genefilter_1.48.1    geneplotter_1.44.0   ggplot2_1.0.0
[22] grid_3.1.2           gtable_0.1.2         Hmisc_3.15-0
[25] iterators_1.0.7      lattice_0.20-29      latticeExtra_0.6-26
[28] locfit_1.5-9.1       MASS_7.3-37          munsell_0.4.2
[31] nnet_7.3-8           plyr_1.8.1           proto_0.3-10
[34] RColorBrewer_1.1-2   reshape2_1.4.1       rpart_4.1-8
[37] RSQLite_1.0.0        scales_0.2.4         sendmailR_1.2-1
[40] splines_3.1.2        stringr_0.6.2        survival_2.37-7
[43] tools_3.1.2          XML_3.98-1.1         xtable_1.7-4
[46] XVector_0.6.0

[alesssia]

Yours, Devon, may be a good guess! I've tried to update 'GenomicRanges', obtaining the following error:

Error : .onLoad failed in loadNamespace() for 'XVector', details:
  call: get(name, envir = asNamespace(pkg), inherits = FALSE)
  error: object 'setDefaultSlotValue' not found
ERROR: lazy loading failed for package 'GenomicRanges'
* removing '/export71/home/aviscont/R/x86_64-unknown-linux-gnu-library/3.1/GenomicRanges'

then installed XVector and (again) GenomicRanges, that also updated the dependencies 'IRanges', 'GenomeInfoDb'. Now we have the same versions of all these packages. However, when loading DESeq2 I obtain the following message:

Error : objects 'metadata', 'isTRUEorFALSE', 'isSingleString' are not exported by 'namespace:IRanges'
Error: package or namespace load failed for 'DESeq2'

error that I obtain also when installing DESeq2 from scratch also when IRanges_2.0.1 is one of the attached packages. Any idea? Thanks a lot!

[Devon Ryan]

No clue there, these sorts of errors are always a real PITA to fix since often more than one package is borked.

Answer 1

[Michael Love]

Just to check, are you installing with biocLite()? If not, definitely always install with biocLite(), and if you are having issues, you should be typing [y] when asked if you want to update your other Bioc packages. See also Upgrading installed Bioconductor packages here http://bioconductor.org/install/#update-bioconductor-packages

[alesssia]

Yeah, I am installing with biocLite() and yeah, I always typed [y] when I was asked to update my other Bioconductor packages. It did not help this time :(

[Michael Love]

Feel free to post this to the Bioc support site: support.bioconductor.org

The Bioc core team has lots of experiences with edge cases and might have an idea what to do. If you do post there, just put a link from here to that post so people can follow the trail. Also, include the biocLite() calls and the sessionInfo().

[alesssia]

Finally, changing the order of the updates I managed to have everything working. Thanks!