[BioC] DESeq2 design

[Michael Love]

On Aug 26, 2014 8:42 PM, "Guest [guest]" <guest at bioconductor.org> wrote:
>
> 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
>

The error here is informing you that the 'conditions' vector should be a
column of the column data, in this case, the 'sampleTable' data.frame.

DESeq2 doesn't use variables from the global environment for the design,
because we need to be sure that the information is tied to the columns of
the count matrix (order, subsetting, etc.), which is accomplished by only
using the columns of colData for the design.

Mike

> 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.

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