I have been trying DESeq2 to analyse my RNAseq data. Data is from sequencing a cell line treated with a drug at different time point intervals. My sampleTable looks like this:
DataFrame with 5 rows and 2 columns treatment time <factor> <factor> cl_0h untreated 0 cl_2h treated 2 cl_4h treated 4 cl_6h treated 6 cl_12h treated 12
I want to find expression change in genes with respect to base line time (0 hour). My design and subsequent commands are as follows, but I get an error at estimateDispersions step:
design(dds) <- formula(~ time + treatment + treatment:time) dds <- estimateSizeFactors(dds) dds <- estimateDispersions(dds) gene-wise dispersion estimates Error in optim(betaRow, objectiveFn, method = "L-BFGS-B", lower = -30, : L-BFGS-B needs finite values of 'fn'Is it because lack of replicates? I tried changing fitType argument but I get the same error. And is my design correct for the above sampleTable ?