gene orders

[Hua Li]

When plotting multiple bam files for the same gene list,  are the gene orders in the heatmap for multiple samples same? Or each heatmap is plotted using its own gene order?

Hua Li

Stowers Institute for Medical Research

[Li Shen]

The heatmaps for each gene list share the same gene order. It would be a bad design or less useful if they each has their own order, right? - Li

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Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
New York, NY 10029
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[Hua Li]

That's what I thought. Just want to confirm. Thanks. 

~ Hua

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[Shmuel Ruppo]

When plotting multiple bam files and using clustering - how is the gene order decided upon?

Is the gene order based upon the clustering of one of the bam files (which one?), and the rest plotted according to it?

Or does setting the gene order take into account all the bam files somehow?

Thanks,

Shmuel

On Tuesday, 29 April 2014 21:09:18 UTC+3, Li Shen wrote:

The heatmaps for each gene list share the same gene order. It would be a bad design or less useful if they each has their own order, right? - Li

On Tue, Apr 29, 2014 at 1:06 PM, Hua Li <hua...@gmail.com> wrote:

When plotting multiple bam files for the same gene list,  are the gene orders in the heatmap for multiple samples same? Or each heatmap is plotted using its own gene order?

Hua Li

Stowers Institute for Medical Research

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[Shmuel Ruppo]

I have found the answer myself, so I am posting it here. In the case of the default algorithm (total), the algorithm maps according to the overall enrichment of the 1st profile . In hierarchical clustering (from the article) "when dealing with multiple NGS samples, the clustering is applied to all of them together. "