Software to visualize complex DGE data sets?

Bio_Red

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Join Date: Mar 2014

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Software to visualize complex DGE data sets?

07-07-2014, 06:30 AM

I have 45 samples which may or may not cluster according to genotype (three de novos assembled using Trinity), time and/or treatment (T0 control only, T1, control and treatment, T2 control and treatment)

With so many aspects to consider, can anyone advise how best to analyse and visualize the DGE data I have (processed through EdgeR), and with what software? I had been looking at PCA clustering and Multi-dimensional scaling with web based applications, including VENNT, EXPANDER AND J-Express, but am new to all this and thought it wise to consult first
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blancha

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07-07-2014, 07:21 AM

I like FactoMineR.
I'm able to generate very informative PCA plots with it.

FactoMineR: Exploratory Multivariate Data Analysis with R

http://factominer.free.fr

FactoMineR, an R package dedicated to multivariate Exploratory Data Analysis
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Bio_Red

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07-10-2014, 11:01 PM

Thank you Blancha
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