Question: Correlation between miRNA and gene expression data from TCGA
0
gravatar for Devyani
2.5 years ago by
Devyani30
India
Devyani30 wrote:

I would like to know how can we find the correlation between miRNA and gene expression data from TCGA. The data available in TCGA for miRNA and gene are in two different units like its RPKM for the gene and reads per million for miRNA.

Thank you

mirna rna-seq correlation tcga • 1.3k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Devyani30
3
gravatar for vakul.mohanty
2.5 years ago by
vakul.mohanty240
United States
vakul.mohanty240 wrote:

You can use Spearman's correlation, its a non-parametric measure of rank correlation. You should be able to get around the problem of different units. Another approach would be to use linear models to test associations instead of using correlations. Hope that helps.

ADD COMMENTlink written 2.5 years ago by vakul.mohanty240

Should both the data be checked for normal distribution before going for lm?

ADD REPLYlink written 2.5 years ago by ssv.bio180

How much I know TCGA data doesn't follow normal distribution.

ADD REPLYlink written 2.5 years ago by Devyani30

I don't think you require data to be normally distributed for a linear regression

ADD REPLYlink written 2.5 years ago by vakul.mohanty240

well, i was thinking that the data (TCGA) is transformed data (normalized). My question is other way round. If data is normalized (assuming that TCGA data in use, is normalized), can you still do lm?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by ssv.bio180

TCGA expression data is generally normalized, though you can also get the count data. Linear regression doesn't require your data to be normally distributed so I think you can use linear regression. If your uncomfortable using regressions you can use a non-parametric test like a Spearman's correlation which is independent of the nature of the distribution (given you have enough power).

ADD REPLYlink written 2.5 years ago by vakul.mohanty240
0
gravatar for Devyani
2.5 years ago by
Devyani30
India
Devyani30 wrote:

Thank you. I will try and let you know.

ADD COMMENTlink written 2.5 years ago by Devyani30
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