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Question: DESeq2 "DESeqDataSetFromMatrix" function has started to give me an error
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gravatar for alextuck
2.4 years ago by
alextuck0
Switzerland
alextuck0 wrote:

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          
 
 
ADD COMMENTlink modified 2.4 years ago by Martin Morgan ♦♦ 20k • written 2.4 years ago by alextuck0

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.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Lorena Pantano90
1

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()?

ADD REPLYlink written 2.4 years ago by Michael Love14k

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. :)

ADD REPLYlink written 2.4 years ago by Lorena Pantano90

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. :)

ADD REPLYlink written 2.4 years ago by Lorena Pantano90
0
gravatar for Martin Morgan
2.4 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

Try validating the version of your installed packages

BiocInstaller::biocValid()

and updating as necessary biocLite() -- several of your packages in this 'devel' installation are out of date.

ADD COMMENTlink written 2.4 years ago by Martin Morgan ♦♦ 20k
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