[BioC] DESeq2, problems using list argument to extract results from DESeq

[Jon Bråte [guest]]

Hi,

I have gene expression from several embryogenesis stages as well as non-reproductive stages. I have done DESeq on my DESeqDataSet and want to extract the results from all the embryogenesis stages vs non-reproductive. 

Heres the error I get:

> resNonReprVsAll = results(dds, contrast=list(c("Early vitellogenesis", "Late vitellogenesis", "Fertilization", "Early cleavage", "Late cleavage", "Early preinversion", "Late preinversion", "Early postinversion", "Late postinversion"), "Non reproductive"))
Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues) : 
  all elements of the contrast as a list of length 2 should be elements of 'resultsNames(object)'

Here's the output of resultsNames(dds):
> resultsNames(dds)
 [1] "Intercept"                     "conditionEarly.vitellogenesis" "conditionLate.vitellogenesis" 
 [4] "conditionFertilization"        "conditionEarly.cleavage"       "conditionLate.cleavage"       
 [7] "conditionEarly.preinversion"   "conditionLate.preinversion"    "conditionEarly.postinversion" 
[10] "conditionLate.postinversion"   "conditionNon.reproductive"    

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

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

other attached packages:
[1] DESeq2_1.4.5              RcppArmadillo_0.4.300.8.0 Rcpp_0.11.1               GenomicRanges_1.16.3     
[5] GenomeInfoDb_1.0.2        IRanges_1.22.8            BiocGenerics_0.10.0      

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

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