DEXSeq estimateDispersions error

[john789]

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...

> cds.exons<-estimateDispersions(cds.exons)
Error in model.frame.default(object, data, xlev = xlev) : 
  variable lengths differ (found for 'condition')

how I got there...

[ann@y90-ln-bioinf5 20140627_Shafiq_Ahmed_Gel_vs_Ml]$ R

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
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Platform: x86_64-redhat-linux-gnu (64-bit)

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[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

I can run the exapmle data though I do get some warnings...

> 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)

sessionInfo()

> 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