Invalid row.names length error (scde.error.models)

[jenzopr]

Hi all, when running scde.error.models on a count table with raw counts, I get the following error after several "Classification:weighted" messages: Error in row.names<-.data.frame(*tmp*, value = value) : invalid 'row.names' length

head(ct) looks like: X94_S62 X43_S29 X53_S32 X32_S22 X58_S35 X27_S18 X73_S47 X63_S38 X83_S55 X88_S59 ENSMUSG00000030105 2 5 72 0 0 34 0 0 0 0 ENSMUSG00000098001 0 0 0 0 0 0 0 0 0 0 ENSMUSG00000065904 0 0 0 0 0 0 0 0 0 0 ENSMUSG00000058979 0 0 0 0 73 0 0 0 0 0 ENSMUSG00000049536 0 0 1 645 0 0 0 0 0 0 ENSMUSG00000027333 0 0 0 0 0 0 0 0 0 0

The initial call was o.ifm = scde.error.models(counts=ct,n.cores = n.cores, threshold.segmentation = T, save.crossfit.plots = F, save.model.plots = F, verbose = 1) I can provide the full count table if neccessary. Maybe someone can point me in a direction :) Best

[JEFworks]

Hi Jens,

It's a bit hard for us to tell what's going on without a trackback. The easiest way may be for you to share your count table with me (text table or RData) if that's possible. You can email me at jeanfan@broadinstitute.org. Let me know. Thanks!

Best, Jean

[jenzopr]

Hi all, hi Jean,

I could solve the issue by running a freshly compiled R-3.2.1: R version 3.2.1 (2015-06-18) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Debian GNU/Linux 7 (wheezy)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] scde_1.99.0 flexmix_2.3-13 lattice_0.20-31

loaded via a namespace (and not attached): [1] Rcpp_0.11.6 RColorBrewer_1.1-2 [3] nloptr_1.0.4 futile.logger_1.4.1 [5] futile.options_1.0.0 Lmoments_1.1-6 [7] tools_3.2.1 lme4_1.1-8 [9] nlme_3.1-121 mgcv_1.8-6 [11] Matrix_1.2-1 SparseM_1.6 [13] RcppArmadillo_0.5.200.1.0 extRemes_2.0-5 [15] stats4_3.2.1 grid_3.2.1 [17] nnet_7.3-10 Biobase_2.28.0 [19] distillery_1.0-1 Rook_1.1-1 [21] BiocParallel_1.2.6 limma_3.24.12 [23] minqa_1.2.4 lambda.r_1.1.7 [25] car_2.0-25 edgeR_3.10.2 [27] pcaMethods_1.58.0 modeltools_0.2-21 [29] MASS_7.3-42 BiocGenerics_0.14.0 [31] splines_3.2.1 RMTstat_0.3 [33] pbkrtest_0.4-2 quantreg_5.11 [35] brew_1.0-6 KernSmooth_2.23-15 [37] rjson_0.2.15 Cairo_1.5-6

The issue above was due to my environment, but I couldn't figure out what exactly caused it. Thanks a lot for your help :)

[JEFworks]

Thanks, Jens! Glad it worked out.