By Darius M. Dziuda
Information Mining for Genomics and Proteomics makes use of pragmatic examples and an entire case research to illustrate step by step how biomedical reports can be utilized to maximise the opportunity of extracting new and priceless biomedical wisdom from information. it really is an exceptional source for college kids and pros concerned with gene or protein expression facts in various settings.
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Extra resources for Data mining for genomics and proteomics: Analysis of gene and protein expression data
Example text
9 Since this technology allows for millions of features to be synthesized on a single microarray, more than one feature can be used to detect each target transcript (gene or exon). This redundancy allows a single gene to be represented by several different oligo sequences (corresponding, for example, to various parts, or exons, of the gene). 1). A probe on an array is for one exon, so different probes representing the same gene may represent different splice variants; it is estimated that some 40 – 60% of human genes may have alternative splice variants (Modrek and Lee 2003).
2 MICROARRAY TECHNOLOGY 23 nonspecific hybridization can be calculated from the MM probes. 3 million features (each feature of the size 11 Â 11 micrometers) and 54,000 probe sets11 (each probe set includes 11 PM/MM probe pairs). HT HG-U1331 PM Array Plate The recently introduced Affymetrix Array Plate technology enables parallel processing of multiple samples on a single plate of arrays. 0 microarray, but allows for simultaneous processing of 24 or 96 samples. 0 chip. The plate arrays include only the perfect match (PM) probes, and most of the probe sets have only nine (rather than eleven) PM probes.
The distance of each probe intensity from the median is used to determine the probe contribution to the average. Data points that are far from the median (potential outliers) contribute less to the average. 19 Saturated probe pairs are excluded from the detection call analysis. If all probe pairs of a probe set are saturated, the probe set is assigned the Present call and the p-value is set to zero. 20 To make the detection call for the probe set, the p-value calculated for the probe set is compared to two significance levels, a1 and a2, 8 < Present DetectionCall ¼ Marginal : Absent 9 if p-value , a1 = if a1 p-value , a2 : ; if p-value !
