[BioC] select CPM value and what does logFC value mean_edgeR

Gordon K Smyth smyth at wehi.EDU.AU
Thu Oct 17 09:12:37 CEST 2013

Dear Naresh,

> Date: Mon, 14 Oct 2013 18:54:48 +0000
> From: Naresh Vasani <nareshvasani at gmail.com>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] select CPM value and what does logFC value mean_edgeR
> Hi Users,
> I have 6 libraries. Can anyone please elaborate how to select CPM value.

You will need to more specific about what you are trying to do.  Are you 
trying to choose a cutoff on which to filter low count genes?  The User's 
Guide gives guidance on this.

> And What does logFC value mean? For e.g In comparison between WT and 40,
> gene54 has logFC value of +3 and gene55 has logFC value of -4.
> Does +3 means gene54 is highly expressed in WT compare to 40.
> Does -4 means gene55 is highly expressed in 40 compare to WT.

Well, it depends on which way around you have compared WT to 40.  If you 
compared WTvs40 (WT minus 40) then, yes, a logFC of 3 means that gene54 is 
2^3=8 times more highly expressed in WT than in 40.

If however you compared 40vsWT then it will be the other way around.

The first line of output from topTags() tells you which way around the 
comparison was done.

Best wishes

> Am I understanding correct?
> I would really appreciate your help.
> Thanks,
> Naresh

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