[BioC] heatmap.2 Z-score vs logFC

[Ochsner, Scott A]

Neel,

You just need to do a little more digging within the help for heatmap.2.  See ?heatmap.2 and read the description of just what applying scale to rows actually does to your values.

Scott Ochsner
Baylor College of Medicine
One Baylor Plaza
Houston, TX 77030  

> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-
> project.org] On Behalf Of Neel Aluru
> Sent: Tuesday, October 18, 2011 10:33 AM
> To: bioconductor at r-project.org
> Subject: [BioC] heatmap.2 Z-score vs logFC
> 
> Hello Bioc Users,
> 
> I am having a hard time understanding why heatmap.2 uses row (or column) Z-
> score instead of directly plotting logFC values?  Based on the formula for
> calculating Z-score, I understand that it is used for scaling or smoothing. But,
> isn't it the same when using logFC. Please correct if I am wrong. I really
> appreciate if anyone can give me a clear explanation.
> 
> Sorry for asking a silly question. I
> 
> --
> Neel Aluru
> Visiting Investigator
> Biology Department
> Woods Hole Oceanographic Institution
> 45 Woods Hole Road
> Woods Hole 02543
> Massachusetts
> USA
> 
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