Then, each pair of matrices that x% of their appearances on the promoter set were overlapping was clustered and the matrix with the lower information content (i.e., the matrix which is less different from a uniform distribution) was removed.
Outlier samples in this distribution were removed as such samples are likely biased for intensity.
After the normalization, the bias distribution was removed in both control and RDX treated samples.
Patients with extreme ADU values at both the low and high ends of the distribution were removed.
Here, 3 data points from the head and 4 data points from the tail of the Flunet distribution were removed to improve the fit.
The results showed that the distributions of gene expressions of 402 genes belong to the common Weibull distribution, whereas the others whose distributions of gene expressions fail to be in the Weibull distribution are removed.
A trimmed mean or truncated mean is a statistical measure of central tendency, where a percent of the high and low ends of a distribution are removed and the mean is calculated using the remaining data of the remaining distribution.
For horizontal (x direction) half-bridge profiles with a single peak, 30 pixels at either end of the distribution were removed to prevent mis-fitting due to variable background signals in that region.
(iii) Filtering out genes with low fold changes (FCs): Genes with log2 FC) < 0.67 × standard deviation (SD) away from the group mean (i.e., between the first and the third quartile assuming that log2 FC) follows a normal distribution) were removed.
For the purpose of quality control, CpG probes with detection p-value above 0.01, those located in sex chromosomes and at SNPs, and those with deviation from bimodal distribution were removed from further analysis.
