Gene expression correlation analysis

Question

[Jenny Han]

Hi! I have 12000 gene expression for 75 individual. And wanna conduct gene expression correlation analysis. Already conducted correlation analysis with R, and I wanna identify distribution about correlation values. How can I draw density plot with this data? (Ignore column, including all values) or recommend other plot.

Answer 1

[Buffo]

I recommend you this answer of Kevin about PCA for rnaseq. I prefer this analysis to summarize a large number of samples more than a simple correlation test.

[Jenny Han]

Thanks for your nice advice :-) But I want to find out gene's correlation rather than sample's correlation. PCA is used to examine sample's clustering, did I understand correctly?

[Buffo]

"Sample´s clustering" yes, based on gene expression. So, samples clustered will have similar expression patterns, exactly what are you looking for.

Answer 2

[Jenny Han]

I solved the problem myself :-)

It was

plot(density(data_name))

with R

[MatthewP]

Hey, can you also post your figure here?