Conditional Quantile Normalization (cqn) error
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@ericmartin-21381
Last seen 2.2 years ago
UCSC

I generated a count list using featureCounts of my ATAC-seq data and fed it into R. I got the GC bias and lenght for each peak queried, and made a list for the sequencing depth. When I run the following command:

ataccountscqn <- cqn(ataccounts0715, x = ataccovar3$gccontent, lengths = ataccovar3$length, sizeFactors = atac.sizefactor, verbose = TRUE)

I get the following error:

Error in qr.default(t(const)) : NA/NaN/Inf in foreign function call (arg 1)

I checked for NAs in the datasets, there aren't any. I checked the types of data in each file to make sure there are numbers and not characters for the values, and a checked the type() of each dataset to make sure it aligns with the sample data. The sample dataset works fine and produces an output, so i'm at a loss as to what (I most likely did wrong) is going on.

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

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

attached base packages: [1] parallel stats4 splines stats graphics grDevices utils datasets [9] methods base

other attached packages: [1] dplyr0.8.3 scales1.0.0 SummarizedExperiment1.14.0 [4] DelayedArray0.10.0 BiocParallel1.18.0 matrixStats0.54.0
[7] Biobase2.44.0 GenomicRanges1.36.0 GenomeInfoDb1.20.0
[10] IRanges
2.18.1 S4Vectors0.22.0 BiocGenerics0.30.0
[13] Matrix1.2-17 readr1.3.1 readxl1.3.1
[16] cqn
1.30.0 quantreg5.42 SparseM1.77
[19] preprocessCore1.46.0 nor1mix1.3-0 mclust_5.4.5

loaded via a namespace (and not attached): [1] bitops1.0-6 DirichletMultinomial1.26.0 TFBSTools1.22.0
[4] bit64
0.9-7 httr1.4.0 backports1.1.4
[7] tools3.6.0 utf81.1.4 R62.4.0
[10] DT
0.7 seqLogo1.50.0 DBI1.0.0
[13] lazyeval0.2.2 colorspace1.4-1 tidyselect0.2.5
[16] bit
1.1-14 compiler3.6.0 cli1.1.0
[19] plotly4.9.0 rtracklayer1.44.0 caTools1.17.1.2
[22] stringr
1.4.0 digest0.6.20 Rsamtools2.0.0
[25] R.utils2.9.0 XVector0.24.0 pkgconfig2.0.2
[28] htmltools
0.3.6 BSgenome1.52.0 htmlwidgets1.3
[31] rlang0.4.0 rstudioapi0.10 RSQLite2.1.1
[34] VGAM
1.1-1 shiny1.3.2 jsonlite1.6
[37] gtools3.8.1 R.oo1.22.0 RCurl1.95-4.12
[40] magrittr
1.5 GO.db3.8.2 GenomeInfoDbData1.2.1
[43] fansi0.4.0 Rcpp1.0.1 munsell0.5.0
[46] R.methodsS3
1.7.1 stringi1.4.3 zlibbioc1.30.0
[49] plyr1.8.4 grid3.6.0 blob1.2.0
[52] promises
1.0.1 crayon1.3.4 miniUI0.1.1.1
[55] CNEr1.20.0 lattice0.20-38 Biostrings2.52.0
[58] annotate
1.62.0 hms0.5.0 KEGGREST1.24.0
[61] zeallot0.1.0 pillar1.4.2 reshape21.4.3
[64] TFMPvalue
0.0.8 XML3.98-1.20 glue1.3.1
[67] BiocManager1.30.4 data.table1.12.2 vctrs0.2.0
[70] png
0.1-7 chromVAR1.6.0 httpuv1.5.1
[73] cellranger1.1.0 MatrixModels0.4-1 tidyr0.8.3
[76] gtable
0.3.0 poweRlaw0.70.2 purrr0.3.2
[79] assertthat0.2.1 ggplot23.2.0 mime0.7
[82] xtable
1.8-4 later0.8.0 viridisLite0.3.0
[85] tibble2.1.3 GenomicAlignments1.20.1 AnnotationDbi1.46.0
[88] memoise
1.1.0

cqn normalization conditionalquantilenormalization atac-seq • 540 views
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Entering edit mode
@kasper-daniel-hansen-2979
Last seen 11 weeks ago
United States

If you send me the input, I can take a slow look.

Best, Kasper (Sent from my phone.)

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