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=form ula(~ 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.

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=formul a(~ 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. [[alternative HTML version deleted]]