question related to RNA seq

[kjaja]

Hi All,

I have RNA sequencing data (expression data) for a control sample and case1 (with disease) and case 2(with a more severe disease)at multiple time points. i.e the expression of each gene is measured at multiple time points for the cases and the control samples. I am a newbie and was wondering if anyone has some advice on how to analyze this type of data?

thanks

[yueluo]

You can take a look at STEM:

http://www.cs.cmu.edu/~jernst/stem/

[kjaja]

thanks, since my data is RNA seq, can I use STEM analyze it? it seems that it is designed for microarray data.

[yueluo]

The input for STEM is normalized gene-expression, so it should be fine.

[blancha]

You could try also try edgeR, an R package, to analyze your time series.