[BioC] edgeR-calcNormFactors

[Wolfgang Huber]

Dear Chris

Apr/23/12 2:50 PM, chris Jhon scripsit::
> Hi All,
>
> I used calcNormFactors function in edgeR to normalize my data :
>
> Normalized->calcNormFactors(data)
>
> However ,when i used it
>
> Normalized1->calcNormFactors(data,refColumn=1)
>
>
> I got slightly different normalization factors,The difference is about 0.02
> between Normalized and Normalized1 for some libraries
> For me it was not expected as i thought the function considers the 1st
> column is the reference column by default.Any Comments??

It's always great to have thoughts, but sometimes it is more precise to 
check what it says in the documentation. For instance, the manual page 
of calcNormFactors says "If 'refColumn' is unspecified, the library 
whose upper quartile is closest to the mean upper quartile is used."

Best wishes
	Wolfgang

> Thank you and best regards
> Chris
>
> 	[[alternative HTML version deleted]]
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber