I ran Combat on 450k data for ~3000 samples and was pleased with the results. However, in order to get the script to run I had to omit any probes with NA values for any sample from the dataset. Due to this, if I want to use the Combat adjusted values for my downstream analysis, I will lose well over half of my data which is not ideal.
I am wondering if someone could assist me in better understanding where I went wrong. Should Combat have run fine in the sva package with the NAs included, was this just an issue with my file? Or, is it true that if I want to use Combat I will unfortunately have to lose any probe with an NA value in any of my samples.
Thank you in advance for your assistance.