[BioC] DESeq2 Error in estimateSizeFactorsForMatrix

[Caleb Bostwick [guest]]

Hello Michael. I am a graduate student neuroscience researcher attempting to use the DESeq2 package to perform differential expression analysis of my sequencing data. I am following the beginner vignette but substituting my own data into the code. I managed to get to the part where it tells me to call the DESeq function, but I received the following error:

> dds <- DESeq(ddsFull)
estimating size factors
Error in estimateSizeFactorsForMatrix(counts(object), locfunc, geoMeans = geoMeans) : 
  every gene contains at least one zero, cannot compute log geometric means

-----

My data was generated from FASTQ files from the sequencer, which I quality/adapter trimmed, and then aligned to our reference genome using the programs STAR and Bowtie2. The unmapped reads from the STAR program were subsequently run through Bowtie2 and the SAM file outputs from both alignment programs were combined using Picard-Tools MergeSAM. The merged SAM files were then converted to BAM files and I began the DESeq2 beginner tutorial. 

Could you please help me or direct me to a source where I might find a solution to my error problem? A "Google search" on the error did not return useful results. Thank you very much.

Best,
Caleb Bostwick

 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] DESeq2_1.4.5            RcppArmadillo_0.4.300.0 Rcpp_0.11.1             GenomicAlignments_1.0.1 BSgenome_1.32.0         Rsamtools_1.16.0        Biostrings_2.32.0       XVector_0.4.0          
 [9] GenomicFeatures_1.16.1  AnnotationDbi_1.26.0    Biobase_2.24.0          GenomicRanges_1.16.3    GenomeInfoDb_1.0.2      IRanges_1.22.7          BiocGenerics_0.10.0     BiocInstaller_1.14.2   

loaded via a namespace (and not attached):
 [1] annotate_1.42.0    BatchJobs_1.2      BBmisc_1.6         BiocParallel_0.6.1 biomaRt_2.20.0     bitops_1.0-6       brew_1.0-6         codetools_0.2-8    DBI_0.2-7          digest_0.6.4      
[11] fail_1.2           foreach_1.4.2      genefilter_1.46.1  geneplotter_1.42.0 grid_3.1.0         iterators_1.0.7    lattice_0.20-29    locfit_1.5-9.1     plyr_1.8.1         RColorBrewer_1.0-5
[21] RCurl_1.95-4.1     RSQLite_0.11.4     rtracklayer_1.24.1 sendmailR_1.1-2    splines_3.1.0      stats4_3.1.0       stringr_0.6.2      survival_2.37-7    tools_3.1.0        XML_3.98-1.1      
[31] xtable_1.7-3       zlibbioc_1.10.0

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