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Machines01:19

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Machines are complex structures consisting of movable, pin-connected multi-force members that work together to transmit forces. One example of a machine is the cutting plier, which is used to cut wires by applying forces to its handles. When equal and opposite forces are exerted on the handles of the cutting plier, they cause the cutting edges to come together and apply equal and opposite reaction forces on the wire, which are greater than the applied forces.
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Making Patch-pipettes and Sharp Electrodes with a Programmable Puller
05:30

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Published on: October 8, 2008

What does PLIER really do?

Terry M Therneau1, Karla V Ballman

  • 1Division of Biostatistics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

Cancer Informatics
|March 5, 2009
PubMed
Summary
This summary is machine-generated.

The PLIER algorithm, despite a biologically questionable assumption, effectively captures key error characteristics. This probe level error function works well by assuming mismatch probes measure only non-specific binding.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Gene Expression Analysis

Background:

  • The Probe Level Intensity Estimation (PLIER) algorithm is widely used for gene expression analysis.
  • Its derivation relies on a biologically implausible assumption, prompting investigation into its effectiveness.

Purpose of the Study:

  • To elucidate the reasons behind the high performance of the PLIER algorithm.
  • To reconcile the algorithm's success with its non-intuitive theoretical underpinnings.

Main Methods:

  • Analysis of the PLIER algorithm's derivation and error function.
  • Evaluation of the assumptions regarding Perfect Match (PM) and Mismatch (MM) probe errors.

Main Results:

  • The PLIER algorithm's probe level error function accurately reflects ideal error characteristics.
  • This accuracy is maintained despite a non-intuitive assumption about PM and MM probe errors.

Conclusions:

  • The PLIER algorithm's success is attributed to its error function's ability to model key aspects of gene expression data.
  • The assumption that mismatch probes measure only non-specific binding and no signal is critical to its performance.