Correlation among genes of RNA-seq samples

[rakscalloni]

Hello!

I have RNA-seq data from two conditions: embryonic stem cells and cardiomyocytes differentiated from them. The data was aligned and the reads were counted using HTSeq.
I want to estimate the correlation among lncRNAs and mRNAs (estimate correlation among genes) expressed in the embryonic stem cells samples. What kind of normalization should I apply on my data to make it read to calculate correlation using pearson/spearman correlation?
I tried the function "varianceStabilizingTransformation" from DESeq2, but I am not quite sure it is the right way to normalize the data in my case.

Thank you

[fanli]

DESeq2's variance stabilizing transform is a good starting point. Clustering or network methods might be another thing to consider if you're looking for relationships among genes.