dmpFinder from minfi package for EPIC array doesn't show beta values

Hi,

I was trying to run dmpFinder from minfi package and I used the following command:

 Sample_Group <- pData(mSetSqFlt)$Sample_Group
 dmp <- dmpFinder(bvals, pheno = Sample_Group, type = "categorical")

The output from the above command gives:

                       intercept          f                    pval       qval
cg00493362  0.866879973 40.43898552 0.00000 0.387257687
cg03825239  0.838860807 38.1071432  0.00000 0.387257687
cg24848890  0.02316834  36.09555835 0.00000 0.387257687
cg09073308  0.839290052 35.16143989 0.00000 0.387257687

But my question is I am not getting beta value (differential methylation) in the above extracted column. Although looking into the minfi protocol with continuous variable it does show beta column also.

Anyone having the same issue or know how to overcome this problem can give suggestions. Any help in this regard is highly appreciated.

Thanks.

r bioconductor

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updated 6.8 years ago by zx8754

• written 6.8 years ago by sinha.puja •

When I wanted to check the methylation profile (beta values) of each tag (resulted by dmpFinder as differentialy methylated) I just merged my input data I mean all tags with beta values with dmpFinder result, then I can select only statistically significant tags. By merging I mean something like:

merge(x = dmp, y = all_tags_with_beta_values, by = "Tag_ID", all.x = TRUE)

But notice that column representing your tags must have the same name in both df's, be also aware about of type of thic column, let it be the same, ex. factor in both cases.

• 0 views • link

written 6.8 years ago by Adamo0_91 •

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