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Gene expression correlation analysis

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.

gene r
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updated by Buffo Buffo • written by Jenny Han • Jenny Han

2 answers

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.

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written by Buffo Buffo

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?

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written by Jenny Han • Jenny Han

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

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written by Buffo Buffo

I solved the problem myself :-)

It was

plot(density(data_name))

with R

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written by Jenny Han • Jenny Han

Hey, can you also post your figure here?

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written by MatthewP MatthewP

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