[BioC] heatmap.2 Z-score vs logFC

[Neel Aluru]

Thank you so much for clarifying. It makes total sense.

Neel

On 10/18/11 11:44 AM, Sean Davis wrote:
> Hi, Neel.
>
> Some rows have larger logFC than others.  Without scaling, those rows
> will be brighter than the rows that have smaller logFC.  Scaling the
> rows (columns) makes the rows (columns) have similar variation so that
> even rows that have smaller logFC still have visible changes when
> plotted.  If most of your rows (columns) have similar variation, then
> scaling will not make much difference.
>
> Sean
>
> On Tue, Oct 18, 2011 at 11:33 AM, Neel Aluru<naluru at whoi.edu>  wrote:
>> 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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-- 
Neel Aluru
Visiting Investigator
Biology Department
Woods Hole Oceanographic Institution
45 Woods Hole Road
Woods Hole 02543
Massachusetts
USA