I tried to run normalizeTMT. I have 13 batches (experiments), two of them have 10 labeled samples and the rest batches have 6 samples. It seems that normalization depends on the number of samples inside batches.
This is how the normalization looks if I take all samples (10 in two experiments and 6 samples in each of the rest):
And this is a plot if I leave 6 samples in each experiment:
Is there a way to normalize data without removing any samples?
I tried to run normalizeTMT. I have 13 batches (experiments), two of them have 10 labeled samples and the rest batches have 6 samples. It seems that normalization depends on the number of samples inside batches.
And this is a plot if I leave 6 samples in each experiment:
This is how the normalization looks if I take all samples (10 in two experiments and 6 samples in each of the rest):
Is there a way to normalize data without removing any samples?