I used DEseq2 for estimation of differentially gene expression in iPS cells and CMs cells
my design was first sample_name cell_type condition SRR1 iPSCs d0 SRR2 iPSCs d0 SRR3 iPSCs d0 SRR1 CMs d15 SRR2 CMs d15 SRR3 CMs d15
I got results properly. dds<- DESeqDataSetFromMatrix(countData = data, colData = pheno, design = ~ cell_type)
I have got fold changes in the results.
I am confused to understand where the gene expression is higher?
may anyone tell me the genes with -ive fold change are downregulated in CMs or iPSCs?
thanks in advance