I am doing Differential methylation analysis between Healthy samples and Glioma samples. I have txt files with beta values but the package minfi I think requires idat files. Please confirm this. If Minfi requires idat files can I use another package like Limma? Does limma work with txt files?
The IDAT files are the raw data (i.e. containing intensity values for the red, green channels, and also information on additional control probes, etc.). If you had them, you could use minfi to import them, normalize your data, calculate the beta values, and then feed them into limma.
If you only have beta values, you can perfectly use them with limma (limma just needs a matrix of features * samples, it doesn't know what the nature of your data is, you can use it for any type of data as long as it meets its assumptions). Just read the tables into R and follow the limma manuals. Only thing to take into account is that you may consider transforming them into M-values (see this), for example with lumi::beta2m.
The only thing about using beta values is that you will have much less control on if and how they were normalized, filtered, and so on.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6