Question: Sample Correlation in RNA-Seq data
0
gravatar for kaihami
4.6 years ago by
kaihami0
Brazil
kaihami0 wrote:

Hello,

I think it might be a very silly question, therefore sorry about my ignorance.

Imagine a RNA-seq data set with n samples, and I want to determine the correlation between each other.

After count normalization, we can perform a correlation between each sample, using Pearson, Spearman, or other one. In a gene to gene correlation I do can understand how these tests works.

But if I have a huge data set (n samples) with m genes, how the correlation test works? Can anybody answer me please?

Regards,

rna-seq correlation • 4.6k views
ADD COMMENTlink modified 4.6 years ago by ethan.kaufman360 • written 4.6 years ago by kaihami0
1
gravatar for ethan.kaufman
4.6 years ago by
ethan.kaufman360
Canada
ethan.kaufman360 wrote:

Correlation is a pairwise measure.  You can calculate correlation between two samples (by considering each gene as an independent observation) but not between n samples.  To get a sense of the overall concordance of your dataset, I would calculate all pairwise correlations, which would generate a symmetric nxn correlation matrix, and should identify any outlier samples.  The corrplot function in R provides a nice heatmap-style visualization of this.

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by ethan.kaufman360

Yeap, a really silly question, I thank you ethan. I don't know why I haven't seen it before lol

ADD REPLYlink written 4.6 years ago by kaihami0
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