ChIPQC: Error in summary.factor
Entering edit mode
Last seen 4.2 years ago

I am tyring to use ChIPQC to check the quality metrics of my ChIPSeq experiment. I am using R version 3.6.0 (2019-04-26) -- "Planting of a Tree" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x8664-w64-mingw32/x64 (64-bit) & BiocManager 1.30.4 & ChIPQC 1.20.0 using the following code, I get the error: DMSONFAT1bio1 NFAT DMSO 1 Narrow Error in Summary.factor(c(1L, 112L, 223L, 334L, 445L, 456L, 467L, 478L, : ‘max’ not meaningful for factors

> samples <- read.csv("meta/SampleSheet.csv")
> samples
         SampleID Tissue Factor Condition Replicate                            bamReads                                          Peaks
1  DMSO_NFAT1bio1     NA   NFAT      DMSO         1 data/bams/DMSO_NFAT1bio1_sorted.bam data/peakcalls/DMSO_NFAT1bio1_peaks.narrowPeak
2  DMSO_NFAT1bio3     NA   NFAT      DMSO         2 data/bams/DMSO_NFAT1bio3_sorted.bam data/peakcalls/DMSO_NFAT1bio3_peaks.narrowPeak
3  DMSO_NFAT2bio1     NA   NFAT      DMSO         1 data/bams/DMSO_NFAT2bio1_sorted.bam data/peakcalls/DMSO_NFAT2bio1_peaks.narrowPeak
4  DMSO_NFAT2bio3     NA   NFAT      DMSO         2 data/bams/DMSO_NFAT2bio3_sorted.bam data/peakcalls/DMSO_NFAT2bio3_peaks.narrowPeak
5  DMSO_NFAT5bio1     NA   NFAT      DMSO         1 data/bams/DMSO_NFAT5bio1_sorted.bam data/peakcalls/DMSO_NFAT5bio1_peaks.narrowPeak
6  DMSO_NFAT5bio3     NA   NFAT      DMSO         2 data/bams/DMSO_NFAT5bio3_sorted.bam data/peakcalls/DMSO_NFAT5bio3_peaks.narrowPeak
7   TAC_NFAT1bio1     NA   NFAT       TAC         1  data/bams/TAC_NFAT1bio1_sorted.bam  data/peakcalls/TAC_NFAT1bio1_peaks.narrowPeak
8   TAC_NFAT1bio3     NA   NFAT       TAC         2  data/bams/TAC_NFAT1bio3_sorted.bam  data/peakcalls/TAC_NFAT1bio3_peaks.narrowPeak
9   TAC_NFAT2bio1     NA   NFAT       TAC         1  data/bams/TAC_NFAT2bio1_sorted.bam  data/peakcalls/TAC_NFAT2bio1_peaks.narrowPeak
10  TAC_NFAT2bio3     NA   NFAT       TAC         2  data/bams/TAC_NFAT2bio3_sorted.bam  data/peakcalls/TAC_NFAT2bio3_peaks.narrowPeak
11  TAC_NFAT5bio1     NA   NFAT       TAC         1  data/bams/TAC_NFAT5bio1_sorted.bam  data/peakcalls/TAC_NFAT5bio1_peaks.narrowPeak
12  TAC_NFAT5bio3     NA   NFAT       TAC         2  data/bams/TAC_NFAT5bio3_sorted.bam  data/peakcalls/TAC_NFAT5bio3_peaks.narrowPeak
1      Narrow
2      Narrow
3      Narrow
4      Narrow
5      Narrow
6      Narrow
7      Narrow
8      Narrow
9      Narrow
10     Narrow
11     Narrow
12     Narrow
> experiment <- ChIPQC(samples, annotation="mm10")
DMSO_NFAT1bio1  NFAT DMSO  1 Narrow
Error in Summary.factor(c(1L, 112L, 223L, 334L, 445L, 456L, 467L, 478L,  : 
  ‘max’ not meaningful for factors

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] ChIPQC_1.20.0               DiffBind_2.12.0             SummarizedExperiment_1.14.1 DelayedArray_0.10.0        
 [5] BiocParallel_1.18.1         matrixStats_0.55.0          Biobase_2.44.0              GenomicRanges_1.36.1       
 [9] GenomeInfoDb_1.20.0         IRanges_2.18.2              S4Vectors_0.22.1            BiocGenerics_0.30.0        
[13] ggplot2_3.2.1              

loaded via a namespace (and not attached):
  [1] amap_0.8-17                               colorspace_1.4-1                          rjson_0.2.20                             
  [4] hwriter_1.3.2                             XVector_0.24.0                            rstudioapi_0.10                          
  [7] ggrepel_0.8.1                             bit64_0.9-7                               AnnotationDbi_1.46.1                     
 [10] splines_3.6.0                             TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2   zeallot_0.1.0                            
 [13] Nozzle.R1_1.1-1                           Rsamtools_2.0.1                           annotate_1.62.0                          
 [16] GO.db_3.8.2                               pheatmap_1.0.12                           graph_1.62.0                             
 [19] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2   compiler_3.6.0                            httr_1.4.1                               
 [22] GOstats_2.50.0                            backports_1.1.4                           assertthat_0.2.1                         
 [25] Matrix_1.2-17                             lazyeval_0.2.2                            TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
 [28] limma_3.40.6                              prettyunits_1.0.2                         tools_3.6.0                              
 [31] gtable_0.3.0                              glue_1.3.1                                GenomeInfoDbData_1.2.1                   
 [34] Category_2.50.0                           reshape2_1.4.3                            systemPipeR_1.18.2                       
 [37] dplyr_0.8.3                               batchtools_0.9.11                         rappdirs_0.3.1                           
 [40] ShortRead_1.42.0                          Rcpp_1.0.2                                TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
 [43] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2   vctrs_0.2.0                               Biostrings_2.52.0                        
 [46] gdata_2.18.0                              rtracklayer_1.44.4                        TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7 
 [49] stringr_1.4.0                             gtools_3.8.1                              XML_3.98-1.20                            
 [52] edgeR_3.26.8                              zlibbioc_1.30.0                           scales_1.0.0                             
 [55] BSgenome_1.52.0                           VariantAnnotation_1.30.1                  hms_0.5.1                                
 [58] RBGL_1.60.0                               RColorBrewer_1.1-2                        yaml_2.2.0                               
 [61] memoise_1.1.0                             biomaRt_2.40.4                            latticeExtra_0.6-28                      
 [64] stringi_1.4.3                             RSQLite_2.1.2                             genefilter_1.66.0                        
 [67] checkmate_1.9.4                           GenomicFeatures_1.36.4                    caTools_1.17.1.2                         
 [70] chipseq_1.34.0                            rlang_0.4.0                               pkgconfig_2.0.3                          
 [73] bitops_1.0-6                              TxDb.Celegans.UCSC.ce6.ensGene_3.2.2      lattice_0.20-38                          
 [76] purrr_0.3.2                               GenomicAlignments_1.20.1                  bit_1.1-14                               
 [79] tidyselect_0.2.5                          GSEABase_1.46.0                           AnnotationForge_1.26.0                   
 [82] plyr_1.8.4                                magrittr_1.5                              R6_2.4.0                                 
 [85] gplots_3.0.1.1                            base64url_1.4                             DBI_1.0.0                                
 [88] pillar_1.4.2                              withr_2.1.2                               survival_2.44-1.1                        
 [91] RCurl_1.95-4.12                           tibble_2.1.3                              crayon_1.3.4                             
 [94] KernSmooth_2.23-15                        progress_1.2.2                            locfit_1.5-9.1                           
 [97] grid_3.6.0                                data.table_1.12.2                         blob_1.2.0                               
[100] Rgraphviz_2.28.0                          digest_0.6.21                             xtable_1.8-4                             
[103] brew_1.0-6                                munsell_0.5.0        
ChIPQC • 765 views
Entering edit mode
Last seen 4.0 years ago

I had the same error. As peakcaller I had "MACS" instead of "macs". I see that you use "Narrow", but I think you should use "narrow".

Hope it works!

PeakCaller: Identifier string for peak caller used. If Peaks is not a bed file, this will determine how the Peaks file is parsed. If missing, will use default peak caller specified in caller parameter. Possible values: – “raw”: text file file; peak score is in fourth column – “bed”: .bed file; peak score is in fifth column – “narrow”: default peak.format: narrowPeaks file – “macs”: MACS .xls file – “swembl”: SWEMBL .peaks file – “bayes”: bayesPeak file – “fp4”: FindPeaks v4


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