Hello,
I was wondering if it is possible to use the minfi package with preprocessed data generated from GenomeStudio .txt output files? I am using publically available data from ArrayExpress and unfortunately do not have access to raw .idat files.
Best, E.
That depends. For a simple test of each CpG, minfi just uses limma. You could do the same without having to use any of the infrastructure in minfi. But if you want to use bumpHunter to find DMRs, then you will need to create an RGset by hand that has all the CpG locations correctly mapped.
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version 2.3.6
Dear James, Thank you for your reply! Yes, I want to used bumphunter. The data files I have contain the following columns from the Genome Studio software output: Target ID, ProbeID_A, ProbeID_B, Avg_beta, Intensity, Signal_A, Signal_B, Detection_pval
From consulting the documentation of Genome Studio, the columns I would be interested in are Signal_A (unmethylated) and Signal_B (methylated probe). Am I right to assume that these would represent the Meth and Unmeth channels in a minfi MethylSet, or are these Red/Green channels?
https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/genomestudio/genomestudio-2011-1/genomestudio-methylation-v1-8-user-guide-11319130-b.pdf
Best, E.
I have never used files like that, so I cannot say what the different columns are. There might be a function in one of the relevant packages (minfi, ChAMP, lumi, illuminaio, etc) that can read that file, but you will probably need to make your own function to put the data into the correct object (like an
RGSet), and then you would be able to proceed from there.