betweenLaneNormalization and calcNormFactors in RUVs

Question

[manish20072013]

I'm analyzing the RNAseq data using the RUVs tutorial. In this tutorial they use two functions,

uq <- betweenLaneNormalization(filtered, which = "upper") 
s <- RUVs(uq, 1:nrow(uq), k = 2, groups)
design <- model.matrix(~x + s$W)
y <- DGEList(counts = filtered, group = x)
y <- calcNormFactors(y, method = "upperquartile")
y <- estimateGLMCommonDisp(y, design)
y <- estimateGLMTagwiseDisp(y, design)
fit <- glmFit(y, design)

First question: Can I use the "median" instead of "upper" in betweenLaneNormalisation because it is giving me a RLE plot better than "upper"?

Second question: If I'm using "median" in above question then is it appropriate to calculate the normalization factor using the "upperquartile"method? If not then what is better option?

Thanks!