Question: RNA Seq- Performing pearson correlation with clinical variables
gravatar for shreev10
11 months ago by
shreev100 wrote:

Hi All,

I am Ashok. I have a question with regards to performing a correlation between RNA seq data and clinical variables. We have a total of 40 samples with well matched clinical annotation. We performed RNA seq and we are trying to correlate the expression data from RNA seq with clinical variables such as Blood pressure, Tumor stage and grade. My questions are:

  1. Is it right to perform these type of correlation? My clinical variable data is normally distributed but I am aware the sequencing data is based on different distribution.

  2. If we can perform this, what type of data should I use? Raw reads or normalized counts?

I would be thankful if you can help me with these questions.

Thank you. Ashok

rna-seq • 505 views
ADD COMMENTlink modified 11 months ago by ewre220 • written 11 months ago by shreev100
gravatar for ewre
11 months ago by
United States
ewre220 wrote:

Maybe spearman correlation between gene expression FPKM value and your clinical variable is a good choice. Also, if you find both gene A and gene B is correlated with, say, blood pressure. You'd better check whether gene A and gene B are correlated or not.

ADD COMMENTlink written 11 months ago by ewre220
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