Question: Gene expression correlation analysis
0
gravatar for Jenny Han
6 months ago by
Jenny Han10
Seoul, South Korea
Jenny Han10 wrote:

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.

R gene • 350 views
ADD COMMENTlink modified 6 months ago by Buffo1.7k • written 6 months ago by Jenny Han10
1
gravatar for Buffo
6 months ago by
Buffo1.7k
Buffo1.7k wrote:

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.

ADD COMMENTlink written 6 months ago by Buffo1.7k

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?

ADD REPLYlink modified 6 months ago • written 6 months ago by Jenny Han10
1

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

ADD REPLYlink written 6 months ago by Buffo1.7k
0
gravatar for Jenny Han
6 months ago by
Jenny Han10
Seoul, South Korea
Jenny Han10 wrote:

I solved the problem myself :-)

It was

plot(density(data_name))

with R

ADD COMMENTlink written 6 months ago by Jenny Han10

Hey, can you also post your figure here?

ADD REPLYlink written 4 weeks ago by MatthewP290
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