First, I apologize if these are dumb questions... I am new to R and Microarray data. That being said, I would appreciate any helpful feedback and/or links.
From what I've read here, it is unusual to remove flagged data-points in limma and I couldn't find any post showing how to do it within the limma package (read.maimages does have a weight function, but it's not for Agilent data). That being said, I'm doing a rotation with someone who prefers such methodology. Thus, I wrote a script that re-formatted the Agilent data with poorly performing probes removed. This means my .txt files now have different lengths, which I believe is causing an error with read.maimages:
Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of items to replace is not a multiple of replacement length
But I would like to take advantage of limma's normalization processes. Is this possible I could reformat the data in another way so those probes are removed? Did I miss something, and eliminating such probe values is actually possible in limma? Is there another package, which may be able to do what I am seeking?
Again, sorry if this seems like a stupid question or if removing flagged values is considered "bad practice." But would really appreciate any feedback on overcoming this issue.