Pca Plot For Microarray Data

Question

[mandar.bobade60]

Hi,

I have microarray (Agilent) data with me. I have done most of the analysis stuff which were required, such as normalization, differential gene expression analysis, mainly did with limma package. Now, I want to generate PCA plot, I have generated too, but with EMA package, as it seems to be very good representation to me. Also, used plot3d package for three-dimensional plot for which legend is not being generated so could not keep this plot.

Following are my 2 questions:

Is EMA package fine for PCA plot? and

How can I interpret this PCA plot?

Answer 1

[Assa Yeroslaviz]

Hi,

I am not familiar with EMA, but you can use several other packages to create a PCA. take a look here