Row names and probe names does not match in topTable output

Row names and probe names does not match in topTable output

0

Hello
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.

Sincerely, Christine


rownames


topTable


limma

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