DBChIP errors
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mali salmon ▴ 350
@mali-salmon-4532
Last seen 2.7 years ago
Israel
Hello list I have tried to run DBChIP in order to compare two IP libraries with no replicates (yes I know, very bad design but this is what I have) While trying to solve the errors I got, I think I have found few bugs 1. In cases where one sample has peaks on a chromosome which is missing from the other sample I got the error below: >dat <- load.data(chip.data.list=chip.data.list, conds=conds, consensus.site=consensus.site, input.data.list=input.data.list, data.type=" AlignedRead",chr.exclusion = extracted[,1],frag.len=100) *reading data...donecomputing normalization factor between ChIP and control samples....................Error in hist.default(x[[chr]][["+"]], breaks = bk.f, plot = FALSE) : 'x' must be numericIn addition: Warning messages:1: In max(y[[x]][["+"]]) : no non-missing arguments to max; returning -Inf2: In max(y[[x]][["+"]]) : no non-missing arguments to max; returning -Inf* In my case I had a single peak on one of the "undefined" chromosomes in sample1, and no peaks on that chromosome for sample 2. After removing this peak from the list, the command run with no problems. 2. Another error I got was when trying to run the following command >dat <- test.diff.binding(dat) *Error in binom.test(x[1], n = x[2], p = x[3], alternative = "two.sided") : 'n' must be a positive integer >= 'x'* I looked for the problematic rows in the "data" object, and found 25 like these: chr10_111494827 0 0 NaN chr10_128493538 0 0 NaN chr11_100503198 0 0 NaN After removing these 25 sites from the original peak list, the command run successfully. Do you have any idea why I got here "0" values although in the original list there are reads mapped to these peaks? Thanks Mali > sessionInfo() \R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ShortRead_1.20.0 Rsamtools_1.14.2 Biostrings_2.30.1 [4] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 [7] DBChIP_1.6.0 DESeq_1.14.0 lattice_0.20-15 [10] locfit_1.5-9.1 Biobase_2.22.0 BiocGenerics_0.8.0 [13] edgeR_3.4.2 limma_3.16.7 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 bitops_1.0-5 [4] DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 [7] grid_3.0.1 hwriter_1.3 latticeExtra_0.6-26 [10] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.1 [13] stats4_3.0.1 survival_2.37-4 tools_3.0.1 [16] XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.6.0 [[alternative HTML version deleted]]
Normalization DBChIP Normalization DBChIP • 574 views
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