[BioC] 转发： Statistical approach to compare differentiall expressed gene lists

[Wolfgang Huber]

Dear Qinghua

I am afraid your question may be too vague. You will need to define more
precisely what you mean by "better". Then, it should be straightforward
to compute a quantitative criterion. It wouldn't be wise to wait for
someone else to define what is "better" for you.

Also, for any analysis method I know of, gene lists depend in a trivial
manner on a cut-off (e.g. for p-value, score...), and if you want to do
something more meaningful than exegesis of someone's cut-off choice,
than I'd suggest to plot ROC curves for both methods, using a reference
set of genes that is enriched for "truely differentially expressed".

Best wishes
	Wolfgang


> Dear all,
> 
> I have identified two lists of differential expressed gene from the
> same expression data but treated with different normalisation
> methods. List A contains 995 genes and list B contains 2400 genes.
> More than nine hundreds genes are overlapped between two lists,
> namely most of genes in list A are also included in list B. The idea
> is to check whether list B is better than list A.
> 
> In addition to visualisation approach (like hierarchical clustering
> heatmap) or biological interpretations,  I am wondering is there any
> other statistical approach available to compare two differential
> expressed gene lists?
> 
> I would appreciate any advice, or pointers to any references for
> this!
> 
> Bests, Qinghua
> 
> 
> 
> ___________________________________________________________ 好玩贺卡等你发，邮
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-- 

Best wishes
      Wolfgang


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