منابع مشابه
Between-array normalization for 450K data
The Illumina Infinium HumanMethylation450 BeadChip is frequently used in epigenetic research. Besides quantile normalization there is currently no standard method to normalize the data between arrays. We describe some properties of the data generated by this platform and present a normalization method based on local regression. We compare the performance of this method with other commonly used ...
متن کاملNormalization of 450K data
> library(normalize450K) > library(minfiData) ## this package includes some .idat files > library(data.table) > path samples = fread(file.path(path, 'SampleSheet.csv'),integer64='character') > samples[,file:=file.path(path,Sentrix_ID,paste0(Sentrix_ID,'_',Sentrix_Position))] > ## samples$file is a character vector containing the location of the > ##...
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When dealing with large scale gene expression studies, observations are commonly contaminated by sources of unwanted variation such as platforms or batches. Not taking this unwanted variation into account when analyzing the data can lead to spurious associations and to missing important signals. When the analysis is unsupervised, e.g. when the goal is to cluster the samples or to build a correc...
متن کاملNormalization of qPCR array data: a novel method based on procrustes superimposition
MicroRNAs (miRNAs) are short, endogenous non-coding RNAs that function as guide molecules to regulate transcription of their target messenger RNAs. Several methods including low-density qPCR arrays are being increasingly used to profile the expression of these molecules in a variety of different biological conditions. Reliable analysis of expression profiles demands removal of technical variati...
متن کاملConsiderations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies.
Analysis of epigenetic mechanisms, particularly DNA methylation, is of increasing interest for epidemiologic studies examining disease etiology and impacts of environmental exposures. The Infinium HumanMethylation450 BeadChip(®) (450K), which interrogates over 480,000 CpG sites and is relatively cost effective, has become a popular tool to characterize the DNA methylome. For large-scale studies...
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ژورنال
عنوان ژورنال: Frontiers in Genetics
سال: 2015
ISSN: 1664-8021
DOI: 10.3389/fgene.2015.00092