error running DESeq2
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@laianavarromartin-7750
Last seen 6.3 years ago
Spain

 

Hi,

I'm running the DESeq function in DESeq2 as follows:

 

ddsRep = DESeqDataSetFromMatrix(countData=countData,

                             colData=colData,
                             design=~ Replicate + Condition)

dds$Condition <- relevel(dds$Condition, "Ctrl")

dds <- DESeq (dds,test = "Wald")

 

The problem is that I'm getting this error:

Error in averagePriorsOverLevels(objectNZ, betaPriorVar) : 

  beta prior for Replicate.T.R1.,Condition.T.1.ppm. is not greater than 0

 

What that exactly means?

deseq2 averagePriorsOverLevels • 1.0k views
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@mikelove
Last seen 4 hours ago
United States

Can you provide you sessionInfo() ?

Also what does colData look like:

as.data.frame(colData(ddsRep))

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So I'm not sure the origin of the error, but you can eliminate it just by setting betaPrior=FALSE when running DESeq().

For some reason the prior is not estimable for one of the coefficients.

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and will this affect my results?

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The results are perfectly valid without the beta prior and this is how nearly all other RNA-seq software return fold changes (without a prior-based moderation).

If you read the DESeq2 paper, we describe how the prior on fold changes ("beta"), is useful for visualization and ranking, but it has little effect on inference (p-values, adjusted p-values).

For whatever reason, the prior could not be estimated for some of your coefficients, so anyway there is not the choice.

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@laianavarromartin-7750
Last seen 6.3 years ago
Spain
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
 [1] Rcmdr_2.2-5                RcmdrMisc_1.0-4            sandwich_2.3-4             car_2.1-2                  GenomicFeatures_1.24.4    
 [6] AnnotationDbi_1.34.4       GenomicAlignments_1.8.4    Rsamtools_1.24.0           Biostrings_2.40.2          XVector_0.12.0            
[11] rnaseqGene_0.99.119361     ggplot2_2.1.0              DESeq2_1.12.3              SummarizedExperiment_1.2.3 Biobase_2.32.0            
[16] GenomicRanges_1.24.2       GenomeInfoDb_1.8.3         IRanges_2.6.1              S4Vectors_0.10.2           BiocGenerics_0.18.0  

   

 

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loaded via a namespace (and not attached):
 [1] nlme_3.1-128                  bitops_1.0-6                  matrixStats_0.50.2            pbkrtest_0.4-6               
 [5] RColorBrewer_1.1-2            httr_1.2.1                    fission_0.106.2               tools_3.3.1                  
 [9] R6_2.1.2                      rpart_4.1-10                  Hmisc_3.17-4                  DBI_0.4-1                    
[13] Gviz_1.16.1                   mgcv_1.8-12                   colorspace_1.2-6              nnet_7.3-12                  
[17] gridExtra_2.2.1               chron_2.3-47                  quantreg_5.26                 airway_0.106.2               
[21] SparseM_1.7                   tcltk2_1.2-11                 rtracklayer_1.32.1            scales_0.4.0                 
[25] genefilter_1.54.2             stringr_1.0.0                 digest_0.6.9                  relimp_1.0-5                 
[29] foreign_0.8-66                minqa_1.2.4                   rmarkdown_1.0                 dichromat_2.0-0              
[33] htmltools_0.3.5               lme4_1.1-12                   PoiClaClu_1.0.2               ensembldb_1.4.7              
[37] BSgenome_1.40.1               readxl_0.1.1                  RSQLite_1.0.0                 BiocInstaller_1.22.3         
[41] shiny_0.13.2                  zoo_1.7-13                    BiocParallel_1.6.2            acepack_1.3-3.3              
[45] VariantAnnotation_1.18.5      RCurl_1.95-4.8                magrittr_1.5                  Formula_1.2-1                
[49] Matrix_1.2-6                  Rcpp_0.12.6                   munsell_0.4.3                 abind_1.4-5                  
[53] stringi_1.1.1                 MASS_7.3-45                   zlibbioc_1.18.0               org.Hs.eg.db_3.3.0           

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[57] plyr_1.8.4                    AnnotationHub_2.4.2           grid_3.3.1                    lattice_0.20-33              
[61] annotate_1.50.0               locfit_1.5-9.1                knitr_1.13                    tcltk_3.3.1                  
[65] geneplotter_1.50.0            biomaRt_2.28.0                XML_3.98-1.4                  evaluate_0.9                 
[69] biovizBase_1.20.0             latticeExtra_0.6-28           data.table_1.9.6              nloptr_1.0.4                 
[73] httpuv_1.3.3                  MatrixModels_0.4-1            gtable_0.2.0                  mime_0.5                     
[77] xtable_1.8-2                  e1071_1.6-7                   class_7.3-14                  survival_2.39-5              
[81] pheatmap_1.0.8                cluster_2.0.4                 sva_3.20.0                    interactiveDisplayBase_1.10.3
[85] BiocStyle_2.0.2 

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