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The number of pairwise alignments that were classified as RNA with a score of > 5 bits was counted, and these counts were binned by ranges of percent identity.
(A) Selection of the upper X% of highest fold changes within binned absolute expression levels The principal parameter for gene expression data stemming from a typical Affymetrix experiment is the average difference intensity (ADI), which is a representation of the absolute expression of a gene.
min ADI, is based on binned data of hundreds of genes across multiple conditions leading to a highly powerful characterization of a given threshold.
The EST sequences were first binned into clusters if they share the same 21 mer tag beginning with ATG or CTG.
When the CVs in the ratios generated using either the control or partially modified cRNA are binned according to the magnitude of the CV, the partially modified cRNA generates more CVs in the less than 20% bins (Figure 6C).
This compression is also observed when the observed ratio is binned according to the magnitude of the fold change (Figure 6D).
We then binned all the traces belonging within a particular BAC and extending 500 bp beyond the end sequence of that BAC.
A count of the number of genes annotated is included in the output, and unannotated genes are binned into the 'unclassified' category, thus providing users with an automated tracking system for genes not annotated.
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