1- In the table ´Normalization method' here says that CPM (counts per million) can be used for gene count comparisons between replicates of the same sample group.
1.1 Does it mean that for eg. we can compare one gene from a sample of group 'control' with same gene of another 'control' sample but that we cannot compare a gene in 'control' sample with same gene in a 'treatment' sample?
1.2 If so, then when looking for a heatmap with CPM values cannot we for e.g. identify genes that seem to have a higher expression in 'treatment' samples than in 'control' samples? Do we need to use a different normalization method?
2- In same table says that CPM cannot be used for within sample comparisons.
2.1 Does it mean we cannot compare different genes of the same sample?
2.2 What if when looking to CPM heatmap it seems one gene is varying more between 'control' and 'treatment' than the other. Can we make this conclusion if heatmap plots CPM values?