DESeq2 design

We are trying to read in htseq count files into the function DESeqDataSetFromHTSeqCount(), however we are experiencing an issue with the design parameter. Please see the code and error below:


> conditions=factor(c("ShhWT", "ShhNULL", "ShhCondMUT"))
> DESeqDataSetFromHTSeqCount(sampleTable,directory=getwd(),design=formula(~ conditions))
Error in DESeqDataSet(se, design = design, ignoreRank) : 
  all variables in design formula must be columns in colData

Our sample table was read in separately and is a data frame with 6 rows and 3 columns:

> sampleTable
  SampleName
1   Shh_het3
2  Shh_null2
3  Shh_flox1
4  Shh_flox2
5  Shh_flox3
6  Shh_flox4
                                                                FileName
1  Sample_Shh_het3_accepted_hits.RG.rmdup.sam.htseq.gene_wise.readcounts
2 Sample_Shh_null2_accepted_hits.RG.rmdup.sam.htseq.gene_wise.readcounts
3 Sample_Shhflox_1_accepted_hits.RG.rmdup.sam.htseq.gene_wise.readcounts
4 Sample_Shhflox_2_accepted_hits.RG.rmdup.sam.htseq.gene_wise.readcounts
5 Sample_Shhflox_3_accepted_hits.RG.rmdup.sam.htseq.gene_wise.readcounts
6 Sample_Shhflox_4_accepted_hits.RG.rmdup.sam.htseq.gene_wise.readcounts
    Metadata
1      ShhWT
2    ShhNULL
3 ShhCondMUT
4 ShhCondMUT
5 ShhCondMUT
6 ShhCondMUT


Any insight on how to specify the design will be helpful.

Thanks,

Anand




 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-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] DESeq2_1.4.5            RcppArmadillo_0.4.400.0 Rcpp_0.11.2            
[4] GenomicRanges_1.16.4    GenomeInfoDb_1.0.2      IRanges_1.22.10        
[7] BiocGenerics_0.10.0    

loaded via a namespace (and not attached):
 [1] annotate_1.42.1      AnnotationDbi_1.26.0 Biobase_2.24.0      
 [4] DBI_0.2-7            genefilter_1.46.1    geneplotter_1.42.0  
 [7] grid_3.1.0           lattice_0.20-29      locfit_1.5-9.1      
[10] RColorBrewer_1.0-5   RSQLite_0.11.4       splines_3.1.0       
[13] stats4_3.1.0         survival_2.37-7      tools_3.1.0         
[16] XML_3.98-1.1         xtable_1.7-3         XVector_0.4.0       


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