Question: betweenLaneNormalization and calcNormFactors in RUVs
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gravatar for manish20072013
22 months ago by
manish200720130 wrote:

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!

ADD COMMENTlink modified 22 months ago • written 22 months ago by manish200720130
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