On the causes of outliers in Affymetrix GeneChip data

Outliers are observed data points that are far from the least squares line. They have unusual values and need to be examined carefully. Though an outlier may result from erroneous data, at other times, it may hold valuable information about the population under study and should be included in the data. Hence, it is crucial to examine what causes a data point to be an outlier.
The z score is used to find outliers or unusual values. It should be noted that any values beyond -2 and +2 are...

An outlier is an observation of data that does not fit the rest of the data. It is sometimes called an extreme value. When you graph an outlier, it will appear not to fit the pattern of the graph. Some outliers are due to mistakes (for example, writing down 50 instead of 500), while others may indicate that something unusual is happening. Outliers are present far from the least squares line in the vertical direction. They have large "errors," where the "error" or residual is the vertical...

When one or more data points appear far from the rest of the data, there is a need to determine whether they are outliers and whether they should be eliminated from the data set to ensure an accurate representation of the measured value. In many cases, outliers arise from gross errors (or human errors) and do not accurately reflect the underlying phenomenon. In some cases, however, these apparent outliers reflect true phenomenological differences. In these cases, we can use statistical methods...

Sometimes, a data set can have a recorded numerical observation that greatly  deviates from the rest of the data. Assuming that the data is normally distributed, a statistical method called the Grubbs test can be used to determine whether the observation is truly an outlier.  To perform a two-tailed Grubbs test, first, calculate the absolute difference between the outlier and the mean. Then, calculate the ratio between this difference and the standard deviation of the sample. This number is...

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...