Entering edit mode
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
Gordon
> Am I understanding correct?
>
> I would really appreciate your help.
>
> Thanks,
> Naresh
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