Question: DEXSeqDataSetFromHTSeq object creation error
0
gravatar for guffanti.alessandro
4.9 years ago by
Italy
guffanti.alessandro0 wrote:

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

 

 

 

 

 

dexseq • 1.4k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by guffanti.alessandro0
2

Is condition.exon a typo when you made this post or is that what you actually used? If the latter, you just want condition:exon.

ADD REPLYlink written 4.9 years ago by Devon Ryan200

Dear Devon, thanks for this, I am going to try immediately. Bizarrely, the PDF reader I use in my PC at home keeps converting ':' in '.' ...

Will let you know,

Alessandro

 

ADD REPLYlink written 4.9 years ago by guffanti.alessandro0
Answer: DEXSeqDataSetFromHTSeq object creation error
0
gravatar for guffanti.alessandro
4.9 years ago by
Italy
guffanti.alessandro0 wrote:

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

Alessandro

 

ADD COMMENTlink written 4.9 years ago by guffanti.alessandro0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 127 users visited in the last hour