A robust measure of correlation between two genes on a microarray

<p>Abstract</p> <p>Background</p> <p>The underlying goal of microarray experiments is to identify gene expression patterns across different experimental conditions. Genes that are contained in a particular pathway or that respond similarly to experimental conditions could be co-expressed and show similar patterns of expression on a microarray. Using any of a variety of clustering methods or gene network analyses we can partition genes of interest into groups, clusters, or modules based on measures of similarity. Typically, Pearson correlation is used to measure distance (or similarity) before implementing a clustering algorithm. Pearson correlation is quite susceptible to outliers, however, an unfortunate characteristic when dealing with microarray data (well known to be typically quite noisy.)</p> <p>Results</p> <p>We propose a resistant similarity metric based on Tukey's biweight estimate of multivariate scale and location. The resistant metric is simply the correlation obtained from a resistant covariance matrix of scale. We give results which demonstrate that our correlation metric is much more resistant than the Pearson correlation while being more efficient than other nonparametric measures of correlation (e.g., Spearman correlation.) Additionally, our method gives a systematic gene flagging procedure which is useful when dealing with large amounts of noisy data.</p> <p>Conclusion</p> <p>When dealing with microarray data, which are known to be quite noisy, robust methods should be used. Specifically, robust distances, including the biweight correlation, should be used in clustering and gene network analysis.</p

Grasping soft tissue by means of vacuum technique

Introduction: A notable characteristic of bariatric surgery is the frequent manipulation of the bowel. The bowel is large, delicate, flexible, and has a natural lubricant on the tissue surface. Therefore the bowel is difficult to grasp and manipulate. Vacuum technique is commonly used in industry for all types of grasping and manipulation. Two types of nozzles that differed slightly in geometry (NT1 and NT2), were reviewed in an experimental set up for pull tests on pig bowels. Materials and methods: An experimental set-up was used to conduct a series of pull tests on pig bowel tissue. The basic principle of the measurements was a Newton's force balance: F-Pmax = Delta p x A. Student t-tests, two-way ANOVA and Wilcoxon signed rank tests were conducted for the statistical analysis of NT1 and NT2 with regard to the maximum pull force (F-Pmax). Results: Concerning NT1 the Newton's force balance could not be confirmed. Concerning NT2 the Newton's force balance could partly be confirmed. For both nozzle types the effect of Delta p on F-Pmax was significant. F-Pmax increases linear in proportion as Delta p increases. This relation between F-Pmax and Delta p was confirmed by the Newton's force balance. Discussion: The results confirm that vacuum technique can be used as a grasp technique for soft organs, particularly the bowels. By means of a clever design of the nozzle a firm grip can be obtained on the bowel segments. Therefore vacuum technique should be studied for further development of instruments, graspers and retractors, to be used in the abdominal area. (c) 2011 IPEM. Published by Elsevier Ltd. All rights reserved