When running DESeq2 1.8.1, I get the following error:
in call to fitDisp, the following arguments contain NA: log_alphaSEXP, log_alpha_prior_meanSEXP
This happens when calling DESeq and varianceStabilizingTransformation.
The perplexing part is that this error is intermittent and apparently occurs at random. Running the exact same code on exact same input over and over again eventually leads to successful finish, as illustrated in the transcript below. Does some part of the calculation use a random number generator to generate starting values (although it would be great if these could always be the same), or is it a bug within compiled code (this apparently random behaviour could be the result of using uninitialized variables)?
Here's a transcript in which I run DESeq on a list of 3 DESeqDataSet objects. This is not a reproducible example (the data are not defined here), it is rather just an illustration of the problem. If necessary, I can create an R session image with just the necessary information and post is somewhere for download.
> lapply(ds.bicov.all.1, class)
$Cortex.vs.Liver
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
$Striatum.vs.Liver
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
$Striatum.vs.Cortex
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
# Running DESeq on the list
# Attempt 1: Error in second analysis
> deseq.all.wald.1 = lapply(ds.bicov.all.1, DESeq, minReplicatesForReplace = Inf)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- standard model matrices are used for factors with two levels and an interaction,
where the main effects are for the reference level of other factors.
see the 'Interactions' section of the vignette for more details: vignette('DESeq2')
estimating size factors
estimating dispersions
gene-wise dispersion estimates
Error in fitBetaWrapper(ySEXP = counts(object), xSEXP = modelMatrix, nfSEXP = normalizationFactors, :
in call to fitBeta, the following arguments contain NA: alpha_hatSEXP
In addition: There were 50 or more warnings (use warnings() to see the first 50)
# Attempt 2: Error in first analysis
> deseq.all.wald.1 = lapply(ds.bicov.all.1, DESeq, minReplicatesForReplace = Inf)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
Error in fitBetaWrapper(ySEXP = counts(object), xSEXP = modelMatrix, nfSEXP = normalizationFactors, :
in call to fitBeta, the following arguments contain NA: alpha_hatSEXP
# Attempt 3: Success
> deseq.all.wald.1 = lapply(ds.bicov.all.1, DESeq, minReplicatesForReplace = Inf)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- standard model matrices are used for factors with two levels and an interaction,
where the main effects are for the reference level of other factors.
see the 'Interactions' section of the vignette for more details: vignette('DESeq2')
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- standard model matrices are used for factors with two levels and an interaction,
where the main effects are for the reference level of other factors.
see the 'Interactions' section of the vignette for more details: vignette('DESeq2')
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- standard model matrices are used for factors with two levels and an interaction,
where the main effects are for the reference level of other factors.
see the 'Interactions' section of the vignette for more details: vignette('DESeq2')
>
sessionInfo()
R version 3.2.2 beta (2015-08-05 r68859)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora 20 (Heisenbug)
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 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] DESeq2_1.8.1 RcppArmadillo_0.5.300.4 Rcpp_0.12.0
[4] GenomicRanges_1.20.5 anRichment_0.79-997 GO.db_3.1.2
[7] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.1 IRanges_2.2.6
[10] S4Vectors_0.6.3 Biobase_2.28.0 BiocGenerics_0.14.0
[13] WGCNA_1.47-3 fastcluster_1.1.16 dynamicTreeCut_1.62
[16] preprocessCore_1.30.0 sva_3.14.0 genefilter_1.50.0
[19] mgcv_1.8-7 nlme_3.1-121 sqldf_0.4-10
[22] RSQLite_1.0.0 DBI_0.3.1 gsubfn_0.6-6
[25] proto_0.3-10 matrixStats_0.14.2 doParallel_1.0.8
[28] iterators_1.0.7 foreach_1.4.2 reshape_0.8.5
[31] Hmisc_3.16-0 ggplot2_1.0.1 Formula_1.2-1
[34] survival_2.38-3 lattice_0.20-33 impute_1.42.0
[37] cluster_2.0.3 class_7.3-13 MASS_7.3-43
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 digest_0.6.8 plyr_1.8.3
[4] chron_2.3-47 futile.options_1.0.0 acepack_1.3-3.3
[7] annotate_1.46.1 rpart_4.1-10 Matrix_1.2-2
[10] splines_3.2.2 BiocParallel_1.2.9 geneplotter_1.46.0
[13] stringr_1.0.0 foreign_0.8-65 munsell_0.4.2
[16] tcltk_3.2.2 nnet_7.3-10 gridExtra_2.0.0
[19] codetools_0.2-14 XML_3.98-1.3 xtable_1.7-4
[22] gtable_0.1.2 magrittr_1.5 scales_0.2.5
[25] stringi_0.5-5 XVector_0.8.0 reshape2_1.4.1
[28] latticeExtra_0.6-26 futile.logger_1.4.1 lambda.r_1.1.7
[31] RColorBrewer_1.1-2 tools_3.2.2 colorspace_1.2-6
Thanks,
Peter
