Question

Pearson's Correlation Coefficient and expression matrix

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5.7 years ago

Morteza Hadizadeh ▴ 60

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.

R • 4.0k views

ADD COMMENT • link updated 5.7 years ago by biobiu ▴ 150 • written 5.7 years ago by Morteza Hadizadeh ▴ 60

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

ADD REPLY • link 5.7 years ago by Buffo ★ 2.4k

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

ADD REPLY • link 5.7 years ago by Morteza Hadizadeh ▴ 60

score 2 · Answer 1 · 2019-03-11

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5.7 years ago

biobiu ▴ 150

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

ADD COMMENT • link 5.7 years ago by biobiu ▴ 150

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Thank you so much for your guidance.

ADD REPLY • link 5.7 years ago by Morteza Hadizadeh ▴ 60