DESeq2 design error

[evenstar]

Hi,

I am trying to run DESeq2 using the "Differential analysis of count data ~ the DESeq2 package provided in the bioconductor website. I want to do an Multi-factor design. I created my count files using HTseq and created a combined table from all the count files.

However I am running in the following error after this step:

> dds <- DESeqDataSetFromMatrix(countData = countDATA,
                             colData = coldata,
                             design = ~ condition + treatment )
Error in DESeqDataSet(se, design = design, ignoreRank) : 
  the model matrix is not full rank, so the model cannot be fit as specified.
  one or more variables or interaction terms in the design formula
  are linear combinations of the others and must be removed

If I try to run the function using only design = ~ condition everything works just fine.

my coldata table:

row.names	condition	type	treatment	autoAntibodies
HS06	        0	0	0	0
HS07        	0	0	0	0
HS10        	0	0	0	0
HS15	        0	0	0	0
HS16	        0	0	0	0
HS17	        0	0	0	0
RITIS01	1	2	1	1
RITIS02	1	2	2	1
RITIS07	1	2	1	1
RITIS09	1	1	1	2
RITIS10	1	2	2	1
RITIS12	1	1	1	2
RITIS14	1	2	1	1
RITIS16	1	1	1	1

I would like to create a full design which takes all the factors into account (condition, type, treatment and autoAntibodies). Could you please explain why the above design does not work.

Thanks,
Even

[dpryan]

If "type", "treatment", and "autoAntibodies" are factors, then "condition" is dictated by them.