Entering edit mode
Hi,
Until a few weeks ago, the DESeq2 function "DESeqDataSetFromMatrix" was working fine for me. However, when I use it now, I get the error, "invalid class “DESeqDataSet” object: 'NAMES' slot must be set to NULL at all time". This can reproduced using the example dataset given on pages 5-6 of the "Analyzing RNA-Seq data with the "DESeq2" package" vignette on the DESeq2 Bioconductor page:
> library("pasilla")
> library("Biobase")
> data("pasillaGenes")
> countData <- counts(pasillaGenes)
> colData <- pData(pasillaGenes)[,c("condition","type")]
> dds <- DESeqDataSetFromMatrix(countData = countData,
+ colData = colData,
+ design = ~ condition)
Error in validObject(.Object) :
invalid class “DESeqDataSet” object: 'NAMES' slot must be set to NULL at all time
I can "fix" this by removing rownames from the countData matrix:
> rownames(countData) <- NULL > dds2 <- DESeqDataSetFromMatrix(countData = countData, + colData = colData, + design = ~ condition)
However, now the DESeq2 function will not run on this DESeqDataSet:
> DESeq(dds2) estimating size factors estimating dispersions gene-wise dispersion estimates Error in DataFrame(...) : different row counts implied by arguments
Can anyone please help?
Thank you!
Alex
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago) 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 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C 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] pasilla_0.9.0 DESeq2_1.9.11 RcppArmadillo_0.5.200.1.0 Rcpp_0.11.6 SummarizedExperiment_0.3.0 Biobase_2.29.1 GenomicRanges_1.21.15 GenomeInfoDb_1.5.8 IRanges_2.3.12 [10] S4Vectors_0.7.7 BiocGenerics_0.15.2 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-2 futile.logger_1.4.1 plyr_1.8.3 XVector_0.9.1 GenomicFeatures_1.21.13 bitops_1.0-6 futile.options_1.0.0 tools_3.2.0 zlibbioc_1.15.0 rpart_4.1-9 [11] biomaRt_2.25.1 digest_0.6.8 annotate_1.47.0 lattice_0.20-31 RSQLite_1.0.0 gtable_0.1.2 DBI_0.3.1 proto_0.3-10 DESeq_1.21.0 gridExtra_0.9.1 [21] genefilter_1.51.0 cluster_2.0.2 rtracklayer_1.29.11 stringr_1.0.0 Biostrings_2.37.2 locfit_1.5-9.1 nnet_7.3-9 grid_3.2.0 AnnotationDbi_1.31.17 survival_2.38-2 [31] XML_3.98-1.2 BiocParallel_1.3.27 foreign_0.8-63 latticeExtra_0.6-26 Formula_1.2-1 geneplotter_1.47.0 ggplot2_1.0.1 reshape2_1.4.1 lambda.r_1.1.7 magrittr_1.5 [41] splines_3.2.0 Hmisc_3.16-0 Rsamtools_1.21.10 scales_0.2.5 GenomicAlignments_1.5.9 MASS_7.3-41 xtable_1.7-4 colorspace_1.2-6 stringi_0.5-2 acepack_1.3-3.3 [51] RCurl_1.95-4.6 munsell_0.4.2 |
it happens to me with a package I am doing when using the develop version of BioC. biocValid() is happy.
I was importing SummarizeExperiment from GenomicRanges. Now there is a new package for that class. I am relative new to BioC as developer, so still don't know what is it. Probably with the devel version of DESeq2 works. In my case, I don't know exactly the problem.
hi Lorena,
Herve has helped to refactor things inside DESeq2 recently, and then I had to rewrite some internal checks last week, but since Monday or so, DESeq2 devel version has build/check without error using the new versions of SE. Can you post your code or a link to where it lives and your sessionInfo()?
thanks Mike! didn't have this problem with DESeq2, only having problem with my package: https://github.com/lpantano/isomiRs/blob/develop/R/AllClasses.R. I will ask Herve help because is far from my knowledge. Although the package is not accepted yet. :)
thanks Mike! didn't have this problem with DESeq2, only having problem with my package: https://github.com/lpantano/isomiRs/blob/develop/R/AllClasses.R. I will ask Herve help because is far from my knowledge. Although the package is not accepted yet. :)