ChIPQC report missing figures
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meeta.mistry ▴ 20
@meetamistry-7355
Last seen 2.5 years ago
United States

Hi,

I am trying to run ChIPQC on my data but for my final report I get blank plots for CrossCoverage and the Signal profile. I don't get any errors when creating the Chip object nor do I get errors when generating the report so it's hard to troubleshoot. 

Here is a link to my report using only chr12 (I get the same for the full dataset) : http://tinyurl.com/chipqc-report

I have below my sample table:

     SampleID Factor Replicate                                   bamReads     ControlID
1  Nanog-Rep1  Nanog        X1  chr12-bam/H1hesc_Nanog_Rep1_chr12_aln.bam  Nanog-Input1
2  Nanog-Rep2  Nanog        X2  chr12-bam/H1hesc_Nanog_Rep2_chr12_aln.bam  Nanog-Input2
3 Pou5f1-Rep1 Pou5f1        X1 chr12-bam/H1hesc_Pou5f1_Rep1_chr12_aln.bam Pou5f1-Input1
4 Pou5f1-Rep2 Pou5f1        X2 chr12-bam/H1hesc_Pou5f1_Rep2_chr12_aln.bam Pou5f1-Input2
                                 bamControl                                  Peaks PeakCaller
1 chr12-bam/H1hesc_Input_Rep1_chr12_aln.bam  chr12-bed/Nanog-rep1_peaks.narrowPeak     narrow
2 chr12-bam/H1hesc_Input_Rep2_chr12_aln.bam  chr12-bed/Nanog-rep2_peaks.narrowPeak     narrow
3 chr12-bam/H1hesc_Input_Rep1_chr12_aln.bam chr12-bed/Pou5f1-rep1_peaks.narrowPeak     narrow
4 chr12-bam/H1hesc_Input_Rep2_chr12_aln.bam chr12-bed/Pou5f1-rep2_peaks.narrowPeak     narrow

I also have the code I ran, including the sessionInfo():

samples <- read.csv('samplesheet_chr12.csv')
chipObj <- ChIPQC(samples, annotation="hg19") 

ChIPQCreport(chipObj, reportName="ChIP QC report: Nanog and Pou5f1", reportFolder="ChIPQCreport", facet=FALSE)

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] ChIPQC_1.10.3              DiffBind_2.2.12            SummarizedExperiment_1.4.0
 [4] Biobase_2.34.0             GenomicRanges_1.26.4       GenomeInfoDb_1.10.3       
 [7] IRanges_2.8.2              S4Vectors_0.12.2           BiocGenerics_0.20.0       
[10] ggplot2_2.2.1             

loaded via a namespace (and not attached):
 [1] Category_2.40.0                           bitops_1.0-6                             
 [3] RColorBrewer_1.1-2                        TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
 [5] UpSetR_1.3.3                              backports_1.1.0                          
 [7] tools_3.3.3                               R6_2.2.1                                 
 [9] KernSmooth_2.23-15                        DBI_0.6-1                                
[11] lazyeval_0.2.0                            colorspace_1.3-2                         
[13] gridExtra_2.2.1                           TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
[15] Nozzle.R1_1.1-1                           sendmailR_1.2-1                          
[17] graph_1.52.0                              TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 
[19] labeling_0.3                              rtracklayer_1.34.2                       
[21] checkmate_1.8.2                           caTools_1.17.1                           
[23] scales_0.4.1                              ChIPseeker_1.10.3                        
[25] BatchJobs_1.6                             genefilter_1.56.0                        
[27] RBGL_1.50.0                               stringr_1.2.0                            
[29] digest_0.6.12                             Rsamtools_1.26.2                         
[31] DOSE_3.0.10                               AnnotationForge_1.16.1                   
[33] XVector_0.14.1                            base64enc_0.1-3                          
[35] plotrix_3.6-5                             limma_3.30.13                            
[37] rlang_0.1.1                               RSQLite_1.1-2                            
[39] BBmisc_1.11                               TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
[41] GOstats_2.40.0                            hwriter_1.3.2                            
[43] BiocParallel_1.8.2                        gtools_3.5.0                             
[45] GOSemSim_2.0.4                            dplyr_0.5.0                              
[47] RCurl_1.95-4.8                            magrittr_1.5                             
[49] GO.db_3.4.0                               Matrix_1.2-10                            
[51] Rcpp_0.12.11                              munsell_0.4.3                            
[53] stringi_1.1.5                             edgeR_3.16.5                             
[55] zlibbioc_1.20.0                           fail_1.3                                 
[57] gplots_3.0.1                              plyr_1.8.4                               
[59] qvalue_2.6.0                              grid_3.3.3                               
[61] gdata_2.17.0                              DO.db_2.9                                
[63] lattice_0.20-35                           Biostrings_2.42.1                        
[65] splines_3.3.3                             GenomicFeatures_1.26.4                   
[67] annotate_1.52.1                           locfit_1.5-9.1                           
[69] knitr_1.16                                fgsea_1.0.2                              
[71] igraph_1.0.1                              boot_1.3-19                              
[73] rjson_0.2.15                              systemPipeR_1.8.1                        
[75] reshape2_1.4.2                            biomaRt_2.30.0                           
[77] fastmatch_1.1-0                           XML_3.98-1.7                             
[79] ShortRead_1.32.1                          latticeExtra_0.6-28                      
[81] data.table_1.10.4                         gtable_0.2.0                             
[83] amap_0.8-14                               assertthat_0.2.0                         
[85] chipseq_1.24.0                            gridBase_0.4-7                           
[87] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2   TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
[89] xtable_1.8-2                              survival_2.41-3                          
[91] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0   pheatmap_1.0.8                           
[93] tibble_1.3.1                              GenomicAlignments_1.10.1                 
[95] AnnotationDbi_1.36.2                      memoise_1.1.0                            
[97] brew_1.0-6                                TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[99] GSEABase_1.36.0  

Any help on this would be great and much appreciated.

Thanks!

Meeta

 

chipqc software error • 556 views
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@thomas-carroll-7019
Last seen 13 months ago
United States/New York/The Rockefeller …
hi Meeta, Could you try providing ChIPQC with a full samplesheet including the columns Tissue and Condition (These can be filled with NA) and replace the replicate with 1 and 2 instead of X1 and X? This may fix the missing plots. If you are still having problems with this then please send me the ChIPQC object (to tc.infomatics@gmail.com) used to generate the report and i will look from there. thank you, tom On Sun, Jun 11, 2017 at 5:26 PM, meeta.mistry [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User meeta.mistry <https: support.bioconductor.org="" u="" 7355=""/> wrote Question: > ChIPQC report missing figures <https: support.bioconductor.org="" p="" 96933=""/>: > > > Hi, > > I am trying to run ChIPQC on my data but for my final report I get blank > plots for CrossCoverage and the Signal profile. I don't get any errors when > creating the Chip object nor do I get errors when generating the report so > it's hard to troubleshoot. > > Here is a *link to my report using only chr12* (I get the same for the > full dataset) : *http://tinyurl.com/chipqc-report > <http: tinyurl.com="" chipqc-report="">* > > I have below my *sample table:* > > SampleID Factor Replicate bamReads ControlID > 1 Nanog-Rep1 Nanog X1 chr12-bam/H1hesc_Nanog_Rep1_chr12_aln.bam Nanog-Input1 > 2 Nanog-Rep2 Nanog X2 chr12-bam/H1hesc_Nanog_Rep2_chr12_aln.bam Nanog-Input2 > 3 Pou5f1-Rep1 Pou5f1 X1 chr12-bam/H1hesc_Pou5f1_Rep1_chr12_aln.bam Pou5f1-Input1 > 4 Pou5f1-Rep2 Pou5f1 X2 chr12-bam/H1hesc_Pou5f1_Rep2_chr12_aln.bam Pou5f1-Input2 > bamControl Peaks PeakCaller > 1 chr12-bam/H1hesc_Input_Rep1_chr12_aln.bam chr12-bed/Nanog-rep1_peaks.narrowPeak narrow > 2 chr12-bam/H1hesc_Input_Rep2_chr12_aln.bam chr12-bed/Nanog-rep2_peaks.narrowPeak narrow > 3 chr12-bam/H1hesc_Input_Rep1_chr12_aln.bam chr12-bed/Pou5f1-rep1_peaks.narrowPeak narrow > 4 chr12-bam/H1hesc_Input_Rep2_chr12_aln.bam chr12-bed/Pou5f1-rep2_peaks.narrowPeak narrow > > *I also have the code I ran, including the sessionInfo():* > > samples <- read.csv('samplesheet_chr12.csv') > chipObj <- ChIPQC(samples, annotation="hg19") > > ChIPQCreport(chipObj, reportName="ChIP QC report: Nanog and Pou5f1", reportFolder="ChIPQCreport", facet=FALSE) > > sessionInfo() > R version 3.3.3 (2017-03-06) > Platform: x86_64-apple-darwin13.4.0 (64-bit) > Running under: OS X Yosemite 10.10.5 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ChIPQC_1.10.3 DiffBind_2.2.12 SummarizedExperiment_1.4.0 > [4] Biobase_2.34.0 GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 > [7] IRanges_2.8.2 S4Vectors_0.12.2 BiocGenerics_0.20.0 > [10] ggplot2_2.2.1 > > loaded via a namespace (and not attached): > [1] Category_2.40.0 bitops_1.0-6 > [3] RColorBrewer_1.1-2 TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2 > [5] UpSetR_1.3.3 backports_1.1.0 > [7] tools_3.3.3 R6_2.2.1 > [9] KernSmooth_2.23-15 DBI_0.6-1 > [11] lazyeval_0.2.0 colorspace_1.3-2 > [13] gridExtra_2.2.1 TxDb.Celegans.UCSC.ce6.ensGene_3.2.2 > [15] Nozzle.R1_1.1-1 sendmailR_1.2-1 > [17] graph_1.52.0 TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 > [19] labeling_0.3 rtracklayer_1.34.2 > [21] checkmate_1.8.2 caTools_1.17.1 > [23] scales_0.4.1 ChIPseeker_1.10.3 > [25] BatchJobs_1.6 genefilter_1.56.0 > [27] RBGL_1.50.0 stringr_1.2.0 > [29] digest_0.6.12 Rsamtools_1.26.2 > [31] DOSE_3.0.10 AnnotationForge_1.16.1 > [33] XVector_0.14.1 base64enc_0.1-3 > [35] plotrix_3.6-5 limma_3.30.13 > [37] rlang_0.1.1 RSQLite_1.1-2 > [39] BBmisc_1.11 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 > [41] GOstats_2.40.0 hwriter_1.3.2 > [43] BiocParallel_1.8.2 gtools_3.5.0 > [45] GOSemSim_2.0.4 dplyr_0.5.0 > [47] RCurl_1.95-4.8 magrittr_1.5 > [49] GO.db_3.4.0 Matrix_1.2-10 > [51] Rcpp_0.12.11 munsell_0.4.3 > [53] stringi_1.1.5 edgeR_3.16.5 > [55] zlibbioc_1.20.0 fail_1.3 > [57] gplots_3.0.1 plyr_1.8.4 > [59] qvalue_2.6.0 grid_3.3.3 > [61] gdata_2.17.0 DO.db_2.9 > [63] lattice_0.20-35 Biostrings_2.42.1 > [65] splines_3.3.3 GenomicFeatures_1.26.4 > [67] annotate_1.52.1 locfit_1.5-9.1 > [69] knitr_1.16 fgsea_1.0.2 > [71] igraph_1.0.1 boot_1.3-19 > [73] rjson_0.2.15 systemPipeR_1.8.1 > [75] reshape2_1.4.2 biomaRt_2.30.0 > [77] fastmatch_1.1-0 XML_3.98-1.7 > [79] ShortRead_1.32.1 latticeExtra_0.6-28 > [81] data.table_1.10.4 gtable_0.2.0 > [83] amap_0.8-14 assertthat_0.2.0 > [85] chipseq_1.24.0 gridBase_0.4-7 > [87] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 > [89] xtable_1.8-2 survival_2.41-3 > [91] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 pheatmap_1.0.8 > [93] tibble_1.3.1 GenomicAlignments_1.10.1 > [95] AnnotationDbi_1.36.2 memoise_1.1.0 > [97] brew_1.0-6 TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 > [99] GSEABase_1.36.0 > > Any help on this would be great and much appreciated. > > Thanks! > > Meeta > > > > ------------------------------ > > Post tags: chipqc, software error > > You may reply via email or visit ChIPQC report missing figures >
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Hi Tom,

Adding the Tissue and Condition columns appears to have solved the problem. Thanks very much!

Best,

Meeta

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