Entering edit mode
Hi all,
I have 20 samples, four genotype , three stimulation with two replicate each sequenced in two batch please see below table.
coldata <- data.frame(row.names=colnames(countdata),genotype,Rep,stimulation,batch)
coldata$group<- factor(paste0(coldata$stimulation,"_",coldata$genotype))
dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~group)
I used group for the design first but as I have sample from two different batch, I also would like to include batch effect into the model. I thought I would include batch as
dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~batch+group)
but I am getting error
the model matrix is not full rank, so the model cannot be fit as specified.
Can somebody help in understanding how can i create design matrix to include batch effect in my design matrix.
I would appreciate any help Thanks
Thanks Michael for reply !
Yes I understood that it would be difficult to model batch and group since it is nested. so I guess using only ~group in design should take care of variance and depth across the sample.
I did pca analysis using vst, I think its the sample looks fine here. please comment your views
I’m unfortunately too busy these days to provide such feedback on analyses. I reserve my support site time for questions about software and try to distinguish between those and questions about analysis. I’d recommend collaborating with a bioinformatician with experience in RNA-seq for more detailed feedback.