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Old 03-25-2014, 06:14 PM   #57
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Location: US

Join Date: Aug 2013
Posts: 123

In pathway analysis or gene set analysis, you may still use absolute expression levels rather than relative expression levels. However, two things make absolute expression analyses less desirable.

First, it is very hard to quantify absolute expression level. The expression measurements are affected by multiple factors other than the actual expression level or abundance, including transcript sequences, length, GC contents etc. These factors are mostly gene/transcript specific, normalization methods donít model all these factor well.
Second, absolute expression levels are not very biologically relevant even if estimated accurately. Different genes, groups or pathways have very different working abundance ranges and dynamics. Therefore, it is less meaningful to compare the absolute expression levels between genes or pathways directly.

On the opposite, relative expression levels can be accurately estimated and are more comparable between genes because all gene specific factors are cancelled out in such measurements, i.e. a gene's expression relative to its own reference level.
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