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@mahmoudfassad14-22068
Last seen 5.1 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
PeakCaller
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
locale:
[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
