[BioC] RNA-Seq/edgeR reproducability between lanes

[Mark Robinson]

Hi Lana,

On May 12, 2011, at 2:38 AM, Lana Schaffer wrote:

> Hi,
> I need to state the reproducibility between sequence lanes for RNA-Seq.
> I don't think that I can print out a normalized set of count data using TMM but
> Just the normalization scale factors?


Well, you can do it manually, something like:

normvals <- t( t(counts) / (lib.size*norm.factor) ) * 1e6

... (1e6 makes it reads per million)  


>  How can I print out the 75th percentile scaled
> Values?  

Similarly:

p75 <- apply(counts,2,quantile,p=.75)
normvals <- t( t(counts) / p75 )


> If I calculate this 75%-ile counts and then calculate the SD?
> Would it be best to us the common dispersion values?

Yes, common dispersion is a good reflection of variation between samples/lanes.  For tech reps that I've seen, common dispersion is low (e.g. less than 0.01).  You may even consider a (Spearman rank) correlation coefficient?

Hope that helps.

Mark


> 
> Lana Schaffer
> Biostatistics, Informatics
> DNA Array Core Facility
> 858-784-2263
> 
> 
> 	[[alternative HTML version deleted]]
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobinson at wehi.edu.au
e: m.robinson at garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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