The genomic profiles of paired tumors were analyzed using the Affymetrix GeneChip® Mapping 50 K Xba Array or Genome-Wide Human SNP Array 6.0 (for one pair), and the data were normalized with ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) algorithm or Partek Genomic Suite, respectively.
As the Bcd variance can be exaggerated in the data normalized by the basic method, we considered the same ensemble of Bcd profiles but normalized by the alternative artificial normalization method, which minimizes variance in the ensemble (see Methods).
Intensity signals data from Genechip® Human Mapping 50 K Xba Array or Genome-Wide Human SNP Array 6.0 were normalized and analyzed using ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Single nucleotide polymorphism [SNP] arrays) algorithm [ 15] or Partek Genomic Suite (Partek Inc., St Louis, MO, USA), respectively.
Expression quantitative trait locus (eQTL) analysis was performed only on the Caucasian samples (n = 153) by linear regression against the SNM normalized expression values (similar results were observed for the alternative normalization).
Because the alternative normalization of an individual MRI to an MRI template, with the subsequent transferring normalization parameters to a corresponding PET image, may provide a higher spatial accuracy than normalization of a PET image to a PET template image, the two normalization methods were tested.
The analysis was repeated using data normalized against the mean instead of a trimmed mean to test performance using an alternative normalization method.
In the case of the decomposition an alternative normalization is necessary.
In this context, it is interesting to note that (when used for text retrieval purposes) the OKA belief function contains a length-normalisation term to minimize the bias of the STD belief function towards the retrieval of longer documents (i.e., larger molecules in the present context) [18]; it may be that an alternative normalization would be appropriate here.
It is called the principal argument, denoted Arg z), with a capital A. (An alternative normalization is 0 ≤ Arg z) < 2π. ) Using trigonometric functions sine and cosine, or the complex exponential, respectively, r and φ are such that the following identities hold: :\begin{array}{lll}z& = & r \left (\cos \varphi + i \sin \varphi\right) \\ & = & r e^{i \varphi}.
Alternative normalization, such as median-centering, did not appreciably affect our results.
