How to interpret fold-changes when the sample purity is not 100%
If your sample purity is less than 100%, it is necessary to take that into account when interpreting the fold-change values.
Given a sample purity of 

fold-change in 100% pure sample![]() |
(29.23) |
For example, if the sample purity is 40%, and you have observed an amplification with a fold-change of 3, then the fold-change in the 100% pure sample would have been:
fold-change in 100% pure sample![]() |
(29.24) |
For a deletion the formula for converting an observed (absolute) fold-change to the actual (absolute) fold change is:
fold-change in 100% pure sample![]() |
(29.25) |
For example, if the sample purity is 40%, and you have a deletion with an absolute fold-change of 1.25, then the absolute fold-change in the 100% pure sample would have been:
fold-change in 100% pure sample![]() |
(29.26) |
Figures 29.27 and 29.28 shows the 'true' fold changes for different observed fold-changes at different sample purities.
Figure 29.27: The true amplification fold-change in the 100% pure sample, for different observed fold-changes, as a function of sample purity.
Figure 29.28: The true deletion fold-change in the 100% pure sample, for different observed fold-changes, as a function of sample purity.