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Analyzing DNA Methylation Microarray Data in R
| Content Provider | Scilit |
|---|---|
| Author | Curry, Edward |
| Copyright Year | 2020 |
| Description | The addition of methyl groups to cytosine residues in DNA forms part of the mechanisms by which cells can regulate their patterns of gene expression. One widely-used approach is based on bisulphite conversion and microarrays, where sodium bisulphite converts unmethylated Cs to Us but affects no change on methylated Cs, then microarray probes can distinguish between targeted sequences with a C in the query CG site or those with a T. The raw data format from Illumina methylation microarrays is the IDAT file. These can be imported into R using the minfi package. As an example to illustrate how simple this can be, let's download some data to try it out on. There is DNA methylation data available in GEO just as there is gene expression data. The next plot it can be important to check is the controlStripPlot. This compares the intensity values of different control probes on the array. Book Name: Introduction to Bioinformatics with R |
| Related Links | https://content.taylorfrancis.com/books/download?dac=C2017-0-68619-5&isbn=9781351015318&doi=10.1201/9781351015318-9&format=pdf |
| Ending Page | 202 |
| Page Count | 14 |
| Starting Page | 189 |
| DOI | 10.1201/9781351015318-9 |
| Language | English |
| Publisher | Informa UK Limited |
| Publisher Date | 2020-10-23 |
| Access Restriction | Open |
| Subject Keyword | Book Name: Introduction To Bioinformatics with R Biochemical Research Dna Methylation Gene Expression Sodium Package Bisulphite Methylation Microarrays |
| Content Type | Text |
| Resource Type | Chapter |
