We often get questions such as these from customers:
“How can I calculate the actual copy number of my samples in Nexus?”
“Is the probe median value the log ratio of the actual copy number?”
“Can I estimate the actual copy number using the probe median values?”
The answer is not a clear yes/no; it is a bit more complicated. The theoretical values for autosomal chromosomes are
One copy gain = log2(3/2) = 0.57 (3 copies vs. 2 copies in reference)
One-copy loss = log2(1/2) = -1
Two-copy gain = log2(4/2) = 1
However in practice, the number of copies is difficult to estimate from the log2 ratio values of a segment due to various reasons; for example, sample-based issues such as polyploidy, mosaicism, contamination with normal samples, tumor necrosis, etc. and array-based issues such as probe dynamic range, hybridization quality, batching, etc.
Agilent arrays have good dynamic range while SNP arrays like Illumina have a smaller range. You can see this in our default settings for one-copy gain/loss for these platforms (see File->Settings and drop down to Illumina). The new Affymetrix OSCHP platform can directly estimate copy number.
Given these caveats, you can estimate copy number using the probe median value for each call. In Nexus, you can get the probe median values from the data table in the Sample Drill Down window (individual sample window). So, if your data is in log2 space, the call has a probe median of about 0.5-0.57 (=log2(3/2)), the platform was Agilent, and this is not a tumor sample, you can say this is a 1 copy gain (3 copies/2) and if the value was approx. 1.0 (=log2(4/2)) you can say this is 2 copy gain (4 copies/2) and so forth 3 copy gain=log2(5/2). For SNP arrays which have a smaller dynamic range, you would make the calls at slightly lower log ratios.
