Correlation among genes of RNA-seq samples

rakscalloni · 05-17-2016, 07:30 AM

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 · 05-17-2016, 08:58 AM

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.

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05-17-2016, 07:30 AM	#1
rakscalloni Member Location: Brazil Join Date: Apr 2014 Posts: 16	Correlation among genes of RNA-seq samples 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

05-17-2016, 08:58 AM	#2
fanli Senior Member Location: California Join Date: Jul 2014 Posts: 198	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.