I want to perform differential expression on counts generated from featureCounts. Each family has different disease. Can we perfrom differential expression across all samples? or since disease is different from family to family, should we perform separately family by family?
Example sample information is like below
I followed the below link for grouping condition and family and get multiple comparisons. Is it ok t proceed like this?
dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata , design = ~ Family + condition)
dds$group <- factor(paste0(dds$Family, dds$condition))
design(dds) <- ~ group dds <- DESeq(dds) resultsNames(dds)
Could you please let me know your suggestions.
Thanks In Advance