I have normalized data that I am trying to filter with HTSFilter. Here is what I tried to run:
filter <- HTSFilter(x = nc, conds = conds, normalization = "none")
nc is a 14543 x 16 dataframe containing genes as row names and library names as column names. Each column of the dataframe is a numeric vector.
conds is a character vector of length 16 that is identical to the names of the column in the data frame. Some names are duplicated which indicates replicate libraries.
The error I get upon running is:
Error in 1:(nbindiv) : argument of length 0
I looked at the Sultan data in the vignette and couldn't really see how my inputs to the function differed other than the fact my values are continuous and the Sultan data is discrete. The function runs fine on the Sultan data.
Looking through the code on GitHub it looks like somehow the
nbindiv variable gets assigned a
numeric(0) somewhere but I couldn't quite figure out why this is happening.
R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8  LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods  base other attached packages:  DESeq2_1.12.4 SummarizedExperiment_1.2.3 GenomicRanges_1.24.3  GenomeInfoDb_1.8.7 magrittr_1.5 HTSFilter_1.12.0  RDAVIDWebService_1.10.0 GOstats_2.38.1 Category_2.38.0  Matrix_1.2-7.1 AnnotationDbi_1.34.4 IRanges_2.6.1  S4Vectors_0.10.3 Biobase_2.32.0 graph_1.50.0  BiocGenerics_0.18.0 ggplot2_2.1.0 loaded via a namespace (and not attached):  Rcpp_0.12.7 XVector_0.12.1 RColorBrewer_1.1-2  plyr_1.8.4 zlibbioc_1.18.0 bitops_1.0-6  tools_3.3.1 rpart_4.1-10 annotate_1.50.1  RSQLite_1.0.0 gtable_0.2.0 lattice_0.20-34  DBI_0.5-1 gridExtra_2.2.1 rJava_0.9-8  DESeq_1.24.0 cluster_2.0.5 genefilter_1.54.2  locfit_1.5-9.1 nnet_7.3-12 grid_3.3.1  data.table_1.9.6 GSEABase_1.34.1 BiocParallel_1.6.6  XML_3.98-1.4 RBGL_1.48.1 survival_2.39-5  foreign_0.8-67 latticeExtra_0.6-28 Formula_1.2-1  limma_3.28.21 GO.db_3.3.0 geneplotter_1.50.0  edgeR_3.14.0 Hmisc_3.17-4 scales_0.4.0  splines_3.3.1 AnnotationForge_1.14.2 xtable_1.8-2  colorspace_1.2-6 acepack_1.3-3.3 RCurl_1.95-4.8  munsell_0.4.3 chron_2.3-47