Entering edit mode
10 months ago
Luisa
•
0
Hello everyone,
I have a very rudimentary question and am happy to just be suggested I go read a package reference! I have a matrix of M values as well as an annotation file. When I join them and filter on UCSC_RefGene_Name I get too few sites associated with the genes I'm interested in. E.g., I know that a particular candidate gene should have ~60 sites associated with it, but my filter cuts out 50 of them. There must be a more elegant and appropriate way of doing this than the bonehead way I am (just good old joining and filtering). Please let me know where I can start looking to find a tutorial?
So your issue is that your filtering removed probes of interest for you ? Have you identified which filter you applied removed those probes ?
Something like this!
It would be helpful if you could share example of those dataframes (d_cpg, annotation), otherwise it would be difficult to reproduce the issue
If you do :
what is the output ?