[BioC] DESeq2 design

[Guest [guest]]

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       


--
Sent via the guest posting facility at bioconductor.org.