Question about normalization to a set of internal standards
Waverley wrote:
Hi, I have a question of the method as how to normalize the data sets according to a set of the internal measurements. For example, I have performed two batches of experiments contrasting two different conditions (positive versus negative conditions): one at a time. 1. each experiment, I measure signals of variable v1 to v100. I want to understand v1 to v100 change under these two contrasting conditions 2. Also I know different variables v101 to v1110, total of 10 of them, although they are different from each other, but they would of the same or similar values under these two contrasting conditions 3. How do I do the internal normalization? How can I use the the variable v101 to v110 values to normalize the measures of v1 to v100 at either positive or negative condition to minimize batch effect? I hope the comparisons of values (v1 to v100) between two different conditions can be more accurate and robust to external noises. In general, I have a couple of matrices of the same dimensions and a reference matrix of values to be used as reference values to be normalize to. How should I do that?
I don't understand your problem well, but in general internal normalization is by and large an attempt to avoid appropriate modeling (e.g., incorporating block effects or certain covariates in a regression model), and results in overstated confidence of the final estimates by not taking into account the imprecision in the normalizing factors. Frank
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University