
Maybe this is very basic, but how do you identify those 500 genes for the heatmap?

.kripa

From: amackey@virginia.edu
Date: Mon, 7 May 2012 11:47:16 -0400
Subject: Re: [BioC] LIMMA: plotMDS
To: kripa777@hotmail.com
CC: bioconductor@r-project.org

All genes contribute to all principle components; some just more than others.  I've found it useful (or perhaps just entertaining) to see heatmaps of the first N (say 10) component loadings, constrained to the 500 genes whose variances contribute most to those components.


-Aaron

On Sun, May 6, 2012 at 7:21 PM, Kripa R <kripa777@hotmail.com> wrote:




Hi I was wondering how I can figure out which genes correspond to each of the principle components ($cmdscale.out). Gene.selection is set to pairwise for the top 500 but I'd like to know exactly which genes are being considered for cmdscale.out[,3], for example.





Thanks for the help!



.kripa

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