Row names and probe names does not match in topTable output
I am using limma to analyze differential methylation on a 850k Illumina array, and set up my model as recommended by the user guide. Today I noticed after running
topTable() that the rownames in the result data frame and the “Name” column does not match. An extract from the output from
topTable() looks like this:
chr pos strand Name cg09840645 chr4 152613181 - cg02827491 cg05161279 chr17 58156411 + cg13790571 cg26508775 chr4 114213574 + cg02296478 cg23550779 chr19 51471364 + cg08083242 cg00391247 chr5 126112230 + cg17185133 cg01799602 chr4 108104446 + cg18057564
I am worried that all my analyses so far has been based on the “wrong” values and genes for each probe. I am wondering which probe name is correct, and best: how to get them to match? I could not find this problem described elsewhere.
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