The two TCGA-02 samples were hybridized directly at Source C. The proposed MSCN was designed to: (i) be applicable to CN estimates from a wide range of technologies including, but not exclusively, microarrays, (ii) provide full-resolution normalized estimates and (iii) normalize each sample independent of the others.
For mRNAs, the RSEM normalized estimated counts were used; this is analogous to using salmon-derived estimated transcript abundances, as described in a recent paper (Soneson et al., 2016).
If spike-ins are available, they can be used to estimate individual cell's RNA content and normalize expression estimates more accurately.
Finally, the qPCR approach utilized here, using gDNA to normalize expression estimates, could provide more reliable results than the typical alternative of normalizing to expression of a single reference gene in any instance where relative expression estimates are needed.
In fact, it is unnecessary to normalize the estimated transmit symbols during the matrix inversion step, but normalization can be deferred to the soft demapper.
To further illustrate the effect of multisource normalization, we zoom in on a small part of the already studied 60 Mb region on Chr 3. In Figure 7, normalized CN estimates from the four sources as well as the combined normalized CNs are depicted for the 400 kb region at 35.2 35.6 Mb.
In summary, only one division operation is necessary to normalize the estimated transmit signal x ̂ i.
Finally, in order to derive a measure of frame complexity that is resolution independent, we normalize the estimate of the number of bits necessary at the reference quantization level by the number of 16 × 16 macroblocks in the frame (frame _num _MB).
We normalized the estimates of pathogen transcript abundance by the ddCT method [65], using the geometric mean CT value of three honey bee housekeeping genes (actin, RPS5, and mGsT) as a reference for pathogen transcript abundance.
To again take into account the effects of heterogeneity in local mutation rates, we normalized our estimates of nucleotide diversity by sequence divergence with D. simulans.
