Entering edit mode
Thank you for your quick reply Simon. I am inexperienced with R and do
not know how to check if all my genes contain a zero in at least one
of the samples. I'm sorry for my ignorance, but if someone would
explain or point me to an explanation of how I could check this, I
will certainly check this. However, I have used the commercial
software CLC Bio to map each sample's reads to our reference genome
and seen the data displayed in an Excel table and I know that at least
some of the genes do not contain a zero in every sample. If this is
the case in my "raw" DESeq2 data, then I made an error somewhere, but
I am following the "beginner" tutorial very carefully and don't know
where I have gone wrong. Thank you for your help.
Best,
Caleb
---------
Dear Caleb
On 30/05/14 16:59, Caleb Bostwick [guest] wrote:
> 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.
For starters, check whether the claim of the error message is actualy
true:
>* Error in estimateSizeFactorsForMatrix(counts(object), locfunc,
geoMeans = geoMeans) :
*>* every gene contains at least one zero, cannot compute log
geometric means
*
Does every gene contain a zero in at least one of the samples? If so,
how comes?
Simon
On Fri, May 30, 2014 at 11:02 AM, Caleb Bostwick <bostwick@ufl.edu>
wrote:
> Hello Michael. I am a 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
>
>
> The posting guide said I should include sessionInfo():
>
>
> >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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