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Then the probes for the human as well as the mouse dataset were converted to official gene symbols, averaging log transformed expression values of multiple probes targeting the same gene.
Expression values of multiple probes targeting a single gene were averaged, resulting in a total of 15 909 distinct genes.
The SAM and PCA analyses of the microarray profiles brought forward multiple probes targeting a group of several species within genus Porphyromonas - P. catoniae, P. gingivalis, P. macacae and P. gulae - as significantly associated with health.
These methods can be divided into: 1) univariate linear regression models, proposed to model the associations between individual CN and GE probes [ 280], 2) multivariate linear regression models, integrating statistical power across multiple probes targeting adjacent genes or chromosomal positions [ 281], and 3) nonlinear regression models.
Univariate linear regression models have been designed to model the associations between individual CN and GE probes [ 26], as well as multiple and/or multivariate linear regression models that combine statistical power across multiple probes targeting adjacent genes or chromosomal positions [ 14, 26 28].
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The number of eQTLs is less than that of corresponding probes because multiple probes target a single locus and some probes are unmapped to the chromosome.
However, we cannot eliminate the possibility that each peak contains more than one probe, and that either hybridization occurs through partial hybrids between a single target and multiple probes, or that multiple probe-target interactions occur within each peak.
This threshold detection using multiple PNA probes targeting APP visualized green puncta in 56% of AD neuronal nuclei compared to 22% in non-diseased and 14% in DS.
The aim of the summarization step in microarray analysis is generally to combine signals from multiple probes, which target the same expression unit, into a single expression index.
When multiple probes were targeted on the same gene (with the same Entrez ID), these data were collapsed onto the Entrez ID, and mean values were computed as the gene expression value.
The limitations reflect suboptimal probe design, e.g. probes hybridizing to multiple map addresses, probes located within repetitive sequences, or probes targeting genomic sequence containing SNPs.
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