I am using DESeq2 to find Differentially expressed genes. I am using the following code:
conds<-c("kd1","kd1","kd2","kd2","GFP","GFP") Design<-data.frame(condition=conds,row.names=paste(conds,rep(c(1,2),3),sep="_")) dds <- DESeqDataSetFromMatrix(countData = assay(se), colData = Design, design = ~ condition) ddsCollapsed <- collapseReplicates( dds, groupby = dds$condition) ddsCollapsed <- DESeq(ddsCollapsed, betaPrior=FALSE)
after running the last line, I get the following:
using pre-existing size factors
found already estimated dispersions, replacing these
gene-wise dispersion estimates
final dispersion estimates
fitting model and testing
In checkForExperimentalReplicates(object, modelMatrix) :
same number of samples and coefficients to fit,
estimating dispersion by treating samples as replicates.
read the ?DESeq section on 'Experiments without replicates'
I don't know what is the problem actually..
could anybody help