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Data were background-corrected, quantile-normalized between the arrays and probes with intensities less than 10% brighter than negative-control probes of each array were filtered.
Any of the omnidirectional signals of the array is filtered accordingly to the estimated DOA angles and as follows: (16).
The microarray data for each array were filtered and normalized as discussed in [ 7].
For each treatment model, the miRNAs present on this array were filtered using stringency criteria of 1.2-fold change (P=0.05).
Raw data from the array were filtered as described in the Methods section for quality control purposes, and 35,690 qualifying SNPs, representing 8,779 transcribed loci crossing all eight samples, survived for the final DASE analysis.
Specifically, gene expression data generated from Affymetrix U133A arrays was filtered based on present/absent calls and BLAST sequence alignment.
Therefore probes with the lowest 40% of mean log2-expression levels across all arrays were filtered out.
The genes that had 100% P-calls and signal detection value of more than 100 in all three arrays were filtered out from the raw hybridization data.
Signal data for all arrays were filtered to remove the ESTs with large standard deviation.
The CNVs from the SNP arrays were filtered to include only the regions with five probes or more.
Furthermore, all common whitethroat arrays were filtered based on the data produced in a Comparative Genome Hybridization, CGH [ 38].
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