DEXSEQ v 1.12.1 estimateDispersions error

Question

[zhangs6]

I ran DEXSEQ v1.10.0 back in May and generated some results. Now when I update to v1.12.1, it starts to give me error after estimateDispersions step dxd=estimateDispersions(dxd)

error message

Error: 1 errors; first error:
  Error in fitBetaWrapper(ySEXP = counts(object), xSEXP = modelMatrix, nfSEXP = normalizationFactors, : in call to fitBeta, the following arguments contain NA: alpha_hatSEXP

For more information, use bplasterror(). To resume calculation, re-call
  the function and set the argument 'BPRESUME' to TRUE or wrap the
  previous call in bpresume().

First traceback:
  23: estimateDispersions(dxd)
  22: estimateDispersions(dxd)
  21: .local(object, ...)
  20: bplapply(splitObject, function(x) {
          estimateDispersionsGeneEst(x, maxit = maxit, quiet = quiet,
              modelMatrix = modelMatrix, niter = 10)
      }, BPPARAM = BPPARAM)
  19: bplapply(splitObject, function(x) {
          estimateDispersionsGeneEst(x, maxit = maxit, quiet = quiet,
              modelMatrix = modelMatrix, niter = 10)
      }, BPPARAM = BPPARAM)
  18: mclapply(X = X, FUN = FUN, ..., mc.set.seed = BPPARAM$setSeed,
          mc.silent = !BPPARAM$verbose, mc.cores = bpworkers

I wonder what caused this error? Bellow is my sessionInfo.

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

locale:
[1] C

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

other attached packages:
 [1] DEXSeq_1.12.1           BiocParallel_1.0.0      DESeq2_1.6.2
 [4] RcppArmadillo_0.4.500.0 Rcpp_0.11.3             GenomicRanges_1.18.3
 [7] GenomeInfoDb_1.2.3      IRanges_2.0.0           S4Vectors_0.4.0
[10] Biobase_2.26.0          BiocGenerics_0.12.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 BBmisc_1.8           BatchJobs_1.5
 [4] Biostrings_2.34.0    DBI_0.3.1            Formula_1.1-2
 [7] Hmisc_3.14-6         MASS_7.3-35          RColorBrewer_1.1-2
[10] RCurl_1.95-4.5       RSQLite_1.0.0        Rsamtools_1.18.2
[13] XML_3.98-1.1         XVector_0.6.0        acepack_1.3-3.3
[16] annotate_1.44.0      base64enc_0.1-2      biomaRt_2.22.0
[19] bitops_1.0-6         brew_1.0-6           checkmate_1.5.0
[22] cluster_1.15.3       codetools_0.2-9      colorspace_1.2-4
[25] digest_0.6.4         fail_1.2             foreach_1.4.2
[28] foreign_0.8-61       genefilter_1.48.1    geneplotter_1.44.0
[31] ggplot2_1.0.0        grid_3.1.0           gtable_0.1.2
[34] hwriter_1.3.2        iterators_1.0.7      lattice_0.20-29
[37] latticeExtra_0.6-26  locfit_1.5-9.1       munsell_0.4.2
[40] nnet_7.3-8           plyr_1.8.1           proto_0.3-10
[43] reshape2_1.4.1       rpart_4.1-8          scales_0.2.4
[46] sendmailR_1.2-1      splines_3.1.0        statmod_1.4.18
[49] stringr_0.6.2        survival_2.37-7      tools_3.1.0
[52] xtable_1.7-4         zlibbioc_1.12.0

In addition, I tried to reinstall DEXSEQ v 1.10.0 and could not find it any more. Which version of bioconductor and R should I download in order to use DEXSEQ v1.10.0?

Shile

[Steve Lianoglou]

I'd suggest posting this over on the bioconductor support forum as (I'm guessing) you'll likely get an answer a bit quicker there, since the developers of this "suite" of packages are (I think) tuned in a bit more closely there.

One thing I'd like to point out, though, is that I think you're installation might be a bit wonky. It looks like many (most(?), all(?)) of your packages are the latest versions, but the latest version of Bioc should be running on R >= 3.1.1. Not sure if it would help to upgrade to that and reinstall all your stuff, but it could be worth a try.