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Question: DESeq2 Error in estimateSizeFactorsForMatrix
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gravatar for Caleb Bostwick
3.3 years ago by
Caleb Bostwick30 wrote:
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 > [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.3 years ago by Michael Love13k • written 3.3 years ago by Caleb Bostwick30
0
gravatar for Michael Love
3.3 years ago by
Michael Love13k
United States
Michael Love13k wrote:
hi Caleb, You can do this: rs <- rowSums( counts(ddsFull) == 0 ) table(rs) This will tabulate the number of genes with 0, 1, 2, ... samples with a zero. Mike On Tue, Jun 3, 2014 at 10:31 AM, Caleb Bostwick <bostwick@ufl.edu> wrote: > 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 >> > > [[alternative HTML version deleted]]
ADD COMMENTlink written 3.3 years ago by Michael Love13k
Hello Michael. I generated the rowSums count and got: > table(rs) rs 4 18820 I think I have 18820 rows (genes) in my data and 4 samples, so as suggested by the original error, it appears all my genes have 0's for their counts. I displayed my ddsFull object data below for reference: > ddsFull class: DESeqDataSet dim: 18820 4 exptData(0): assays(1): counts rownames(18820): gene0 gene1 ... gene9998 gene9999 rowData metadata column names(0): colnames(4): LE005merged.bam LE006merged.bam LE007merged.bam LE008merged.bam colData names(2): run pheno So I suppose the next question is how do I find and fix the problem of getting 0's for all my gene counts? I am not sure if I need to supply my session info again, but I will below. Thanks for your help. Best, Caleb > 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 [3] 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 [4] GenomicAlignments_1.0.1 BSgenome_1.32.0 Rsamtools_1.16.0 [7] Biostrings_2.32.0 XVector_0.4.0 GenomicFeatures_1.16.1 [10] AnnotationDbi_1.26.0 Biobase_2.24.0 GenomicRanges_1.16.3 [13] GenomeInfoDb_1.0.2 IRanges_1.22.7 BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] annotate_1.42.0 BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.1 [5] biomaRt_2.20.0 bitops_1.0-6 brew_1.0-6 codetools_0.2-8 [9] DBI_0.2-7 digest_0.6.4 fail_1.2 foreach_1.4.2 [13] genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.0 iterators_1.0.7 [17] 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 [25] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 survival_2.37-7 [29] tools_3.1.0 XML_3.98-1.1 xtable_1.7-3 zlibbioc_1.10.0 On Tue, Jun 3, 2014 at 10:41 AM, Michael Love <michaelisaiahlove@gmail.com> wrote: > hi Caleb, > > You can do this: > > rs <- rowSums( counts(ddsFull) == 0 ) > table(rs) > > This will tabulate the number of genes with 0, 1, 2, ... samples with a > zero. > > Mike > > > > On Tue, Jun 3, 2014 at 10:31 AM, Caleb Bostwick <bostwick@ufl.edu> wrote: > >> 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 >>> >> >> > [[alternative HTML version deleted]]
ADD REPLYlink written 3.3 years ago by Caleb Bostwick30
hi Caleb, (I thought I already had an internal check for a user supplying a matrix of all zeros, to provide a more helpful error message, but I guess I'll have to include it in the next version) On Fri, Jun 6, 2014 at 10:17 AM, Caleb Bostwick <bostwick at="" ufl.edu=""> wrote: > Hello Michael. I generated the rowSums count and got: > >> table(rs) > rs > 4 > 18820 > > I think I have 18820 rows (genes) in my data and 4 samples, so as suggested > by the original error, it appears all my genes have 0's for their counts. I > displayed my ddsFull object data below for reference: > You can inspect the counts of a dds with: head(counts(dds)) Or of a SummarizedExperiment with: head(assay(se)) >> ddsFull > class: DESeqDataSet > dim: 18820 4 > exptData(0): > assays(1): counts > rownames(18820): gene0 gene1 ... gene9998 gene9999 > rowData metadata column names(0): > colnames(4): LE005merged.bam LE006merged.bam LE007merged.bam LE008merged.bam > colData names(2): run pheno > > > So I suppose the next question is how do I find and fix the problem of > getting 0's for all my gene counts? > > Perhaps you are counting reads using a different annotation for chromosome names as the genome to which the reads were aligned, i.e. 'chr1' vs '1'. In the beginner vignette we use a GTF file. So on the command line you could look at the chromosome names in the GTF file compared to the reads in the BAM file. Mike > > I am not sure if I need to supply my session info again, but I will below. > Thanks for your help. > > Best, > Caleb > >> 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 > [3] 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 > [4] GenomicAlignments_1.0.1 BSgenome_1.32.0 Rsamtools_1.16.0 > [7] Biostrings_2.32.0 XVector_0.4.0 GenomicFeatures_1.16.1 > [10] AnnotationDbi_1.26.0 Biobase_2.24.0 GenomicRanges_1.16.3 > [13] GenomeInfoDb_1.0.2 IRanges_1.22.7 BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] annotate_1.42.0 BatchJobs_1.2 BBmisc_1.6 > BiocParallel_0.6.1 > [5] biomaRt_2.20.0 bitops_1.0-6 brew_1.0-6 > codetools_0.2-8 > [9] DBI_0.2-7 digest_0.6.4 fail_1.2 foreach_1.4.2 > [13] genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.0 > iterators_1.0.7 > [17] 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 > [25] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 > survival_2.37-7 > [29] tools_3.1.0 XML_3.98-1.1 xtable_1.7-3 > zlibbioc_1.10.0 > > > On Tue, Jun 3, 2014 at 10:41 AM, Michael Love <michaelisaiahlove at="" gmail.com=""> > wrote: >> >> hi Caleb, >> >> You can do this: >> >> rs <- rowSums( counts(ddsFull) == 0 ) >> table(rs) >> >> This will tabulate the number of genes with 0, 1, 2, ... samples with a >> zero. >> >> Mike >> >> >> >> On Tue, Jun 3, 2014 at 10:31 AM, Caleb Bostwick <bostwick at="" ufl.edu=""> wrote: >>> >>> 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 at="" 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 >>> >>> >> >
ADD REPLYlink written 3.3 years ago by Michael Love13k
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