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MiRABELLE predictions and enrichment of downregulated targets were not significantly affected by the normalization algorithm used.
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The normalization algorithm is available from the authors upon request.
The normalization algorithm we use is based on trimmed means rather than on the total or average intensities, because fragments of transcripts affected by the treatment have to be excluded from the calculation of a normalization factor [ 20].
We suspect that the underlying null distributions are adversely effected by failures of the normalization algorithms to properly account for the abnormal feature level characteristics identified by [ 5].
Within one analysis set spot intensities were normalized by the vertical normalization algorithm implemented in the Delta2D software.
Raw expression intensity was background subtracted and normalized by the average normalization algorithm as implemented in GenomeStudio Gene Expression Module v1.0 application software (Illumina).
Raw probe intensities for all treatment conditions were normalized by the quantile normalization algorithm [ 29] using GenomeStudio software from Illumina and log-2 transformed expression obtained for analyses.
Each HRRP sample is normalized by L2 normalization algorithm to avoid the amplitude-scale sensitivity.
MiRNA microarray was normalized by Lowess normalization algorithm using GeneSpring 10.0 (Agilent Technologies, Foster City, CA, USA).
One process that can introduce discrepancies between the results produced by different platforms is the selection of the appropriate normalization algorithm.
Briefly, raw intensity data was corrected by background subtraction in the Genome Studio module and normalized using the Quantile normalization algorithm.
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