Error in vecseq when running estimateTechnicalNoise

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Dear chicagoTeam,

I am trying to use Chicago for analysis of CaptureC data. However, when I am running chicagoPipeline, I am getting an error message (see below). Do you have any idea why this and how I can fix it? I have not found the source code for estimateTechnicalNoise, otherwise I guess that I could just make the suggested changes (i. e. allow.cartesian)?

Thanks a lot for your help Best wishes Angelika Feldmann


*** Running estimateTechnicalNoise...

Estimating technical noise based on trans-counts... Binning baits based on observed trans-counts... Defining interaction pools and gathering the observed numbers of trans-counts per pool... Computing the total number of possible interactions per pool... Preparing the data.....Error in vecseq(f__, len__, if (allow.cartesian || notjoin) NULL else as.integer(max(nrow(x), : Join results in 52261470 rows; more than 27846218 = max(nrow(x),nrow(i)). Check for duplicate key values in i, each of which join to the same group in x over and over again. If that's ok, try including j and dropping by (by-without-by) so that j runs for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please search for this error message in the FAQ, Wiki, Stack Overflow and datatable-help for advice.


sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)


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

other attached packages: [1] Chicago_0.2.9 data.table_1.9.4 argparser_0.3 devtools_1.8.0

loaded via a namespace (and not attached): [1] Rcpp_0.11.6 Formula_1.2-1 cluster_2.0.1 [4] xml2_0.1.1 magrittr_1.5 MASS_7.3-40 [7] splines_3.2.1 munsell_0.4.2 colorspace_1.2-6 [10] lattice_0.20-31 stringr_1.0.0 plyr_1.8.3 [13] tools_3.2.1 nnet_7.3-9 grid_3.2.1 [16] gtable_0.1.2 Delaporte_2.2-3 latticeExtra_0.6-26 [19] git2r_0.10.1 matrixStats_0.14.2 rversions_1.0.2 [22] survival_2.38-1 digest_0.6.8 gridExtra_0.9.1 [25] RColorBrewer_1.1-2 reshape2_1.4.1 ggplot2_1.0.1 [28] acepack_1.3-3.3 rpart_4.1-9 curl_0.9.1 [31] memoise_0.2.1 stringi_0.5-5 scales_0.2.5 [34] Hmisc_3.16-0 foreign_0.8-63 chron_2.3-47 [37] proto_0.3-10

Comments (2)

  1. Mikhail Spivakov

    Dear Angelika, Thanks very much for your interest in Chicago and for your report. This error message usually results from situations where there are many-to-many relationships between the two datasets being joined. It's possible that your data is different from the samples we've been working with in some respect. Perhaps you could share with us a toy example triggering this error? Or, if it's not obvious, perhaps we could chat about it in more detail by email ( Best wishes, Mikhail

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