Genex features

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Genex features

Postby rgandhi » Wed Oct 05, 2011 7:45 pm

Dear Support Group,

I have few questions regarding the use of Genex.

1) Can we normalize data in Genex using quantile method as we use in R program.

2) Is it possible to plot principal component against age of samples. Can we choose principal components in our analysis?

3) When we load Log2 transformed file into the Genex. The "difference" between groups obtained after statistical test like T test or descriptive statistics represent the log2 difference or the linear difference in between the two groups.

Posts: 15
Joined: Wed Jul 06, 2011 7:08 pm

Re: Genex features

Postby Mikael Kubista » Sat Oct 08, 2011 7:30 pm

Quantile normalization is used to correct for certain signal drift when analyzing microarray data. It is not used in qPCR. But as the number of microarray users is growing it is may one day appear

GenEx does not offer a plot of principal components vs. eg. An explanatory variable such as age. But its easy to do. When you perform PCA click the button “view scores”. This displays the scores ina spreadsheet and the data can be save or copied to excel to make the requested plot. To view the loadings you first click the radio button”Loadings” and then you can display the loadings in a spreadsheet. Be aware there is more powerful method for multivariable regression than PCA, which is Partial Least Squares (PLS). PLS is available in GenEx.

When performing t-test in GenEx data are plotted in linear as well as in logarithmic scale. These plots appear when normal view is used (the check box “P-value compact view” shall be left empty)

Good luck
Mikael Kubista
Posts: 455
Joined: Tue Jul 01, 2008 12:28 pm

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