Hi All
I'm getting the following error when trying to run DEXSeq's estimateDispersions() and I can't see how I may have got something the wrong length, though I'm not sure what 'condition' is. Could someone help me sort it out please?
the error...
how I got there...
I can run the exapmle data though I do get some warnings...
sessionInfo()
I'm getting the following error when trying to run DEXSeq's estimateDispersions() and I can't see how I may have got something the wrong length, though I'm not sure what 'condition' is. Could someone help me sort it out please?
the error...
Code:
> cds.exons<-estimateDispersions(cds.exons) Error in model.frame.default(object, data, xlev = xlev) : variable lengths differ (found for 'condition')
Code:
[ann@y90-ln-bioinf5 20140627_Shafiq_Ahmed_Gel_vs_Ml]$ R R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] > library(DEXSeq) Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > list.files(recursive=T,pattern="dexseq_count.out") [1] "E2_GEL_CGATGT_L001_L002_R1/dexseq_count.out" [2] "E2_ML_ATCACG_L001_L002_R1/dexseq_count.out" [3] "G7_GEL_TGACCA_L001_L002_R1/dexseq_count.out" [4] "G7_ML_TTAGGC_L001_L002_R1/dexseq_count.out" [5] "R10_GEL_######_L001_L002_R1/dexseq_count.out" [6] "R10_ML_CAGATC_L001_L002_R1/dexseq_count.out" [7] "R15_GEL_GCCAAT_L001_L002_R1/dexseq_count.out" [8] "R15_ML_ACAGTG_L001_L002_R1/dexseq_count.out" [9] "R24_GEL_TAGCTT_L003_L004_R1/dexseq_count.out" [10] "R24_ML_GATCAG_L003_L004_R1/dexseq_count.out" [11] "R9_GEL_CTTGTA_L003_L004_R1/dexseq_count.out" [12] "R9_ML_GGCTAC_L003_L004_R1/dexseq_count.out" [13] "S2_GEL_AGTTCC_L003_L004_R1/dexseq_count.out" [14] "S2_ML_AGTCAA_L003_L004_R1/dexseq_count.out" > dexseq.input<-list.files(recursive=T,pattern="dexseq_count.out") > patient<-factor(c(1,1,2,2,3,3,4,4,5,5,6,6,7,7)) > treat<-factor(c(rep(c("GEL","ML"),7)), levels=c("GEL","ML")) > metadata<-data.frame(patient,treat) > metadata patient treat 1 1 GEL 2 1 ML 3 2 GEL 4 2 ML 5 3 GEL 6 3 ML 7 4 GEL 8 4 ML 9 5 GEL 10 5 ML 11 6 GEL 12 6 ML 13 7 GEL 14 7 ML > cds.exons<-read.HTSeqCounts(dexseq.input,metadata,flattenedfile="/usr/local/db/Homo_sapiens.GRCh37.70.dexseq.gff") > cds.exons<-estimateSizeFactors(cds.exons) > sizeFactors(cds.exons) E2_GEL_CGATGT_L001_L002_R1/dexseq_count.out 1.2077521 E2_ML_ATCACG_L001_L002_R1/dexseq_count.out 1.0615008 G7_GEL_TGACCA_L001_L002_R1/dexseq_count.out 1.1879558 G7_ML_TTAGGC_L001_L002_R1/dexseq_count.out 1.1544027 R10_GEL_######_L001_L002_R1/dexseq_count.out 1.0404924 R10_ML_CAGATC_L001_L002_R1/dexseq_count.out 0.7823007 R15_GEL_GCCAAT_L001_L002_R1/dexseq_count.out 0.9656107 R15_ML_ACAGTG_L001_L002_R1/dexseq_count.out 1.0358146 R24_GEL_TAGCTT_L003_L004_R1/dexseq_count.out 1.0007947 R24_ML_GATCAG_L003_L004_R1/dexseq_count.out 0.8065910 R9_GEL_CTTGTA_L003_L004_R1/dexseq_count.out 0.9446503 R9_ML_GGCTAC_L003_L004_R1/dexseq_count.out 1.1146453 S2_GEL_AGTTCC_L003_L004_R1/dexseq_count.out 1.1618312 S2_ML_AGTCAA_L003_L004_R1/dexseq_count.out 0.9371032 > cds.exons<-estimateDispersions(cds.exons) Error in model.frame.default(object, data, xlev = xlev) : variable lengths differ (found for 'condition') > dim(counts(cds.exons)) [1] 643455 14 > dim(metadata) [1] 14 2
Code:
> if(suppressWarnings(require("pasilla", quietly=TRUE, character.only=TRUE))){ + + data("pasillaExons", package="pasilla") + pasillaExons <- estimateSizeFactors( pasillaExons ) + pasillaExons <- estimateDispersions( pasillaExons ) + head( fData(pasillaExons)$dispBeforeSharing ) + + } .... Done [1] NA NA NA NA NA NA There were 50 or more warnings (use warnings() to see the first 50)
Code:
> sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-redhat-linux-gnu (64-bit) 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] pasilla_0.2.19 DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.1 AnnotationDbi_1.24.0 biomaRt_2.18.0 [4] Biostrings_2.30.1 bitops_1.0-6 DBI_0.3.0 [7] DESeq_1.14.0 genefilter_1.44.0 geneplotter_1.40.0 [10] GenomicRanges_1.14.4 grid_3.0.2 hwriter_1.3.1 [13] IRanges_1.20.7 lattice_0.20-29 RColorBrewer_1.0-5 [16] RCurl_1.95-4.3 Rsamtools_1.14.3 RSQLite_0.11.4 [19] splines_3.0.2 statmod_1.4.20 stats4_3.0.2 [22] stringr_0.6.2 survival_2.37-7 tcltk_3.0.2 [25] tools_3.0.2 XML_3.98-1.1 xtable_1.7-3 [28] XVector_0.2.0 zlibbioc_1.8.0 > ?estimateDispersions Help on topic ‘estimateDispersions’ was found in the following packages: Package Library DEXSeq /usr/lib64/R/library BiocGenerics /usr/lib64/R/library