DNA Methylation in R
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pbachali ▴ 50
@pbachali-9651
Last seen 4.5 years ago

Hi, everybody. I am Prat working as a Bioinformatician. I am first time analyzing methylation data. I am not familiar with this data at all. I did some literature search and see that IDAT files are required to analyze. I believe these are similar to CEL files but not exactly the CEL files. IDAT files are raw data for methylation data. For example, I am trying to look at the methylation data for this GSE79237 dataset. This is ILLUMINA methylation450k platform. I downloaded the TAR file, but I don't see any IDAT files. I have only .csv file and .txt file. I am not sure how to proceed with this. Were these csv and txt files are normalized data. I dont see any sample filenmaes in that file. And also I am trying to use minfi package in R. My question how to analyze methyaltion data without IDAT files? Is there any way to achieve this?

Any help is much appreciated.  

minfi • 2.2k views
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@james-w-macdonald-5106
Last seen 7 days ago
United States

You could also download the GSE79237_methyl_and_unmethylated_signal_Annotated_AA_vs_EA.txt.gz file and unzip that. Inside you will find a text file that has the betas, as well as the methylated and unmethylated values.

Analyzing those data would be a non-trivial task because you would have to figure out how to get those data into the proper minfi object by hand. An alternative would be to use minfi's getGenomicRatioSetFromGEO, which would appear to be the more reasonable course of action in this instance.

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pbachali ▴ 50
@pbachali-9651
Last seen 4.5 years ago

Thank you for the help. Are there any other packages which can analyse beta values other than minfi?

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If you have a comment or question for a post, please use the ADD COMMENT button. The 'Add your answer' box below is for adding answers, not additional questions.

On the package landing page, at the top left is a set of package views. Under 'BiologicalQuestion' there is DifferentialMethylation, which will show you all the methylation-specific packages.

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