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Old 04-15-2013, 12:03 PM   #1
bioinfor
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Location: houston

Join Date: Mar 2011
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Question How to normalize the RNA seq data for the purpose of correlation analysis

For the purpose of finding differentially expressed genes, there are methods such as DEseq and cuffdiff. It was said that DEseq is better choice for this purpose.

Now I am going to do correlation analysis using RNA seq data, to find gene pairs that significantly correlate with each other. For this purpose, I wonder whether I can use the pre-processed and normalized results from DEseq or cuffdiff ? Actually, I want to do the correlation analysis between miRNA and mRNA based on RNA seq data.
Does anyone have any idea about this?
Thanks.
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