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Eye blink artifacts were mathematically corrected based on a model artifact computed from a minimum of 50 individual artifacts in each participant using the procedure implemented in Scan 4.3 (Neuroscan™, Inc., El Paso, TX, USA) and remaining artifacts were manually dismissed.
PCA was performed using the procedure implemented in the R function ' prcomp'.
The MSA is generated automatically using the procedure implemented in ConSurf-DB (Goldenberg et al., 2009).
For each simulated scenario we computed the percentage of significant tests using the procedure implemented in ARLEQUIN (i.e., assuming an isochronous sampling scheme).
Presence of null alleles at each locus and sample was tested using the procedure implemented by microchecker with a 99% confidence interval (Van Oosterhout et al. 2004).
The redundancy between protein families was checked by using the procedure implemented in the CDART algorithm [ 17] and not more than 2 protein families from the same CDD cluster were retained in the final test set.
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7, 17 Thresholds were applied using the adaptive procedure implemented in the edge function in the Image Processing Toolbox for MATLAB, resulting in a binary image with 1's where the function finds edges in the image and 0's elsewhere.
The null hypothesis of panmixia (rD = 0) was tested using the reshuffling procedure implemented in the software (500 randomizations).
Variance estimates in all analyses described herein were performed using the REML procedure implemented in the nlme package in R [ 42- 44].
Microarray intensity Cel files were background corrected and quantile normalized using the rma2 procedure implemented in the R package affy [ 41, 42].
To identify genes that discriminate between BRCA1- and BRCA2-associated tumors, supervised univariate analyses of array-based log2 gene expression were performed for each clone treating the modified Student t-test as the primary analysis [ 19] using the SAM procedure implemented in open source software, version 2.1.0 (http://www.r-project.org/).org/
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