Hi to everybody! I'll explain my problem. I have two matrices with data from illumina 850 methylation chip. The person that performed the analysis, gave me a matrix with beta values with cytosine names for rows and samples for columns. My problem is that among the cytosines, there are also the control probes that I want to remove. At the moment, I have two matrices: the one explained above and another one with the annotation, with cytosines for rows and all the metadata for columns. The number of rows of course is different because the control probes are not annotated.
My question is: using R, how can I compare the two matrices checking for the presence of unique row names in the beta value matrix, so the control probes, that are not present in annotation matrix? The aim is to find all the cytosines in the beta values that are not present in annotation so to remove them. Thank you for your help!