[BioC] Voom and CQN input

Ryan rct at thompsonclan.org
Tue Nov 26 08:01:39 CET 2013

Given that voom is not restricted to integer values, is there any 
reason one couldn't simply apply the normalization manually before 
calling voom on the data?

On Mon Nov 25 16:53:02 2013, Heather Estrella wrote:
> This is in regards to a previous post by Dr. Gordon Smyth from June, 2012.
> https://stat.ethz.ch/pipermail/bioconductor/2012-June/045950.html
> In the previous post, Dr. Smyth stated:
> "voom() isn't currently setup to accept the normalization matrix from cqn,
> but it will be down the track."
> Does anyone know whether voom() can now accept CQN normalized output? I was not able to find anything in the limma user documentation on whether voom can now handle CQN normalized data as input. I'm trying to correct for sample-specific variability prior to running voom normalization and limma differential expression. I have been reading publications on sample-specific technical variability (e.g. Risso, et al.  BMC Bioinformatics 2011). Is it still recommended to do within-lane quantile normalization prior to differential expression? My data is RNA-Seq from Illumina HiSeq using standard Illumina processing. I definitely have the random hexamer priming issue, but that should (theoretically at least) be consistent across samples for a single gene as Dr. Smyth points out in the previously referenced post.
> Any insight would be great.
> Kind regards,
> Heather
> 	[[alternative HTML version deleted]]
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