[BioC] DESeq2 design
Guest [guest]
guest at bioconductor.org
Tue Aug 26 20:42:48 CEST 2014
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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