I have been provided 30 samples (15 pairs). Each pair has one cancer and one normal sample. They are paired-end sequencing data for 15 cancer and 15 normal samples. I am doing RNA-seq analysis for these samples using DESeq package. I used HTSeq_count to count the number of reads for each gene.
Group1 - Sample1 is cancer and Sample2 is normal
Group2 - Sample3 is cancer and Sample4 is normal
Group3 - Sample5 is cancer and Sample6 is normal
Group15- Sample29 is cancer and Sample30 is normal
The technician asked me to compare each group (1cancer and 1normal) individually. So, I have to perform 15 pairwise comparisons.
1) Is my pair (1 cancer and 1 normal) considered as biological replicates?