Dear Bioconductor Community,
i would like to ask a very specific and short question about the "basic" methodology behind the arrayWeights() function from the package limma. Although, from previous discussions from related posts and also from the original article, i understand that empirical array quality weights mainly "adjust" samples of low quality, which could cause unusual/exaggerated high variance-characterized by computing an overall quality performance from all samples, based on the heteroscedastic model described in the paper
-could also the specific methodology downweights samples, from which unexpected variance is due to other "supplementary biological reasons": ??
for instance, accounting for inter-tumor heterogeneity when having samples from different patients which contribute to the same anatomic location or tissue(etc) ? and/or even for tumor heteroscedacity ?
Or the case is clearly due to various problems relating to sample quality ??
Please excuse me for this naive question, but im currently writting a report and i would not like to include any irrelevant misconceptions about the description of this methodology!!