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Interpreting PCA Graph for Gene Expression - Principle Component Analysis in Gene Expression (Jun/08/2008 )

Hi all,

Usually in analysis of Gene Expression (with n-genes and k-samples) using PCA (Principle Component Analysis)
people generate a plot with "Component 1" as X-axis and "Componenent 2" for Y-axis (and so forth).

I am wondering from this plot what can we say about the particular gene expression dataset?
I mean for biological analysis how can we make use of this graph?

Does the Component-k refers to the Sample-k?

I've looked at this posting but it is still unclear.
http://www.bioinformaticszen.com/2007/08/meaning-from-pca/

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-foolishbrat-

QUOTE (foolishbrat @ Jun 8 2008, 06:49 AM)
Hi all,

Usually in analysis of Gene Expression (with n-genes and k-samples) using PCA (Principle Component Analysis)
people generate a plot with "Component 1" as X-axis and "Componenent 2" for Y-axis (and so forth).

I am wondering from this plot what can we say about the particular gene expression dataset?
I mean for biological analysis how can we make use of this graph?

Does the Component-k refers to the Sample-k?

I've looked at this posting but it is still unclear.
http://www.bioinformaticszen.com/2007/08/meaning-from-pca/

- fb



Perhaps one of the lectures here may resolve your quandary:
http://search.vadlo.com/b/q?sn=158621799&a...lysis&rel=2
http://search.vadlo.com/b/q?sn=158621799&a...array&rel=0

.. cc

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