Dear colleagues:

I keep getting the same error when creating a simple DEXSeqDataSetFromHTSeq object and I really do not understand why. May you help ? I did not find too much help from previous posts in the forum.

The error message is always the same:

Error in DESeqDataSet(se, design, ignoreRank = TRUE) :
  all variables in design formula must be columns in colData

Here is a typical example of my trials

> sampleTable
                        sample condition
Sample_1.DEXSEQ.txt   Sample_1   Fertile
Sample_4.DEXSEQ.txt   Sample_4   Fertile
Sample_58.DEXSEQ.txt Sample_58   Sterile
Sample_86.DEXSEQ.txt Sample_86   Sterile

> countFiles
[1] "/analysis/ANALYSIS_OLD/WTA_KMCE/FASTQ/Sample_1.DEXSEQ.txt"
[2] "/analysis/ANALYSIS_OLD/WTA_KMCE/FASTQ/Sample_4.DEXSEQ.txt"
[3] "/analysis/ANALYSIS_OLD/WTA_KMCE/FASTQ/Sample_58.DEXSEQ.txt"
[4] "/analysis/ANALYSIS_OLD/WTA_KMCE/FASTQ/Sample_86.DEXSEQ.txt"

> flattenedFile
[1] "/analysis/ANALYSIS_OLD/WTA_KMCE/FASTQ/Homo_sapiens.GRCh38.76.gff"

> dxd = DEXSeqDataSetFromHTSeq(
+ countfiles=countFiles,
+ sampleData=sampleTable,
+ design =~ sample + exon + condition.exon,
+ flattenedfile=flattenedFile)
Error in DESeqDataSet(se, design, ignoreRank = TRUE) :
  all variables in design formula must be columns in colData

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-redhat-linux-gnu (64-bit)

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

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

other attached packages:
 [1] DEXSeq_1.10.8           BiocParallel_0.6.1      DESeq2_1.4.5
 [4] RcppArmadillo_0.4.400.0 Rcpp_0.11.2             GenomicRanges_1.16.4
 [7] GenomeInfoDb_1.0.2      IRanges_1.22.10         Biobase_2.24.0
[10] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] annotate_1.42.1      AnnotationDbi_1.26.0 BatchJobs_1.3
 [4] BBmisc_1.7           biomaRt_2.20.0       Biostrings_2.32.1
 [7] bitops_1.0-6         brew_1.0-6           checkmate_1.4
[10] codetools_0.2-9      DBI_0.3.0            digest_0.6.4
[13] fail_1.2             foreach_1.4.2        genefilter_1.46.1
[16] geneplotter_1.42.0   grid_3.1.0           hwriter_1.3.2
[19] iterators_1.0.7      lattice_0.20-29      locfit_1.5-9.1
[22] RColorBrewer_1.0-5   RCurl_1.95-4.3       Rsamtools_1.16.1
[25] RSQLite_0.11.4       sendmailR_1.1-2      splines_3.1.0
[28] statmod_1.4.20       stats4_3.1.0         stringr_0.6.2
[31] survival_2.37-7      tools_3.1.0          XML_3.98-1.1
[34] xtable_1.7-4         XVector_0.4.0        zlibbioc_1.10.0

Thanks a lot in advance !

Alessandro

It worked like a charm. I am now analyzing my NGS dataset. Thanks a lot for your help,

Alessandro