Beta Matrix Input Using MMBC

epigen / RnBeads

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Beta Matrix Input Using MMBC #43

Open sjthursby opened 1 year ago

sjthursby commented 1 year ago

Hi all,

Thank you for updating RnBeads to work on the MMBC array, this is very helpful!

I wanted to import a beta matrix I had from the MMBC array into RnBeads using the "infinitum.data.files" option in rnb.run.import. However, I keep getting stuck at the "Read table with betas" logger output with an error that says "in match.probes2annotation(probes, target, assembly): probes contain invalid IDs.

Please can you help me discover what I am doing wrong.

Many thanks!

schmic05 commented 1 year ago

Hi @sjthursby

Sorry for the late reply. We were trying to figure out the issue, but couldn't do so for now. Can you tell us where you got the data from? It might be due to some inconsistencies with the probe IDs introduced for the MMBC array. We don't have too much experience with it and will try to figure out what is the best way to handle data files as input.

Best,

Michael

sjthursby commented 1 year ago

The beta matrix was an output from the Sesame package. I love all the graphing capabilities from RnBeads but my PI wanted me to use Sesame for the normalization. Raw idats from the same data can be imported into RnBeads without error but the beta matrix from Sesame results in the error mentioned above. Thank you for your help.

schmic05 commented 1 year ago

Great, thanks for the prompt reply. Can you maybe show us how the rows (CpGs) of the input matrix are named?

sjthursby commented 1 year ago

Here is a snapshot of the beta matrix I am trying to import.

schmic05 commented 1 year ago

Thanks a ton, we'll try to solve the issue ASAP.