Dear All,

I try to use CQN package to normalize RNAseq data for modeling, but
could not find CQN vignette at Bioconductor website.

The example from the manual is not clear to me (shown below). I should be
able to run the code by replacing montgomery.subset with our dataset, but
it is not the case.

I assume montgomery.subset is the data set, what is sizeFactors.subset ?
Other pacakge (DESeq, edgeR) will calculate sizeFactors. How about uCovar ?
I Should provide dataset, the package will calculate whatever required by
the package. The explanations are not clear to me.

I would appreciate it if anyone provide guidance on this.

Thanks,
Xin Davis




data(montgomery.subset)
data(sizeFactors.subset)
data(uCovar)
cqn.subset <- cqn(montgomery.subset, lengths = uCovar$length,
x = uCovar$gccontent, sizeFactors = sizeFactors.subset, verbose = TRUE)

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