Pearson's Correlation Coefficient and expression matrix

Question

[Morteza Hadizadeh]

Hi every one,

I have an expression matrix, the rows contain 550 mutual DEGs and columns contain 73 samples (550*73), samples are divided into 2 groups (control and case), 30 sample for control and 43 samples for the case. I want to calculate Pearson's Correlation Coefficient for each group to construct a co-expression network.

I would be grateful if you could guide me to do it.

[Buffo]

What about MDS? I think that to your purpose it would be more illustrative/explanative..

[Morteza Hadizadeh]

Mutual differential expression genes contain up and down-regulated genes.

Answer 1

[biobiu]

Use the function cor in R. You have a good example here.

[Morteza Hadizadeh]

Thank you so much for your guidance.