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Here we report an algorithm to infer CNV haplotypes and individuals' diplotypes at multiple loci from noisy microarray data, utilizing the probability that a signal intensity may be derived from different underlying copy numbers or genotypes.
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Microarray data utilized in this study are stored in the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/) with accession number E-MEXP-3201 E-MEXP-3201 E-MEXP-3201
Our microarray data utilized the Affymetrix ATH1 chip and are from hybridizations described in detail in [ 31].
Statistical analysis of the microarray data utilized Bayesian analysis of variance for microarrays (BAM), using BAMarray software (http://www.bamarray.com) [ 27].
More recently, studies by Woodfine et al. [ 18, 19] confirmed the cytogenetic data, utilizing a microarray approach.
Finally, the resulting values could be applied, in principle, to any data utilizing any of the microarray platforms included in this experiment.
For the successful application of SSM to this short time-series microarray data, we utilized all the replicates on the array for the parameter estimation of SSM.
The method of microarray data analysis utilized here used not only statistical comparisons but also considered biological properties of the data [ 26] in order to find unbiased results covering the entire genome.
RNA-sequencing data were obtained for sexual development (Wang et al. 2014), whereas microarray data were utilized for colony development (Kasuga and Glass 2008) and a time course of conidiation (Greenwald et al. 2010).
Although both SAM (Significance Analysis of Microarray, [ 8]) and LIMMA (Linear Models for Microarray Data, [ 9]) utilize moderated t-statistic and do not need the assumption of rigorous normality, their sensitivity is generally affected by a non-normal distribution.
Microarray data is also utilized to give annotation of REGs, that have been predicted as cis-regulatory elements dependent of promoter position in our previous analysis.
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