Question: Using expression array data to predict ethnicty
0
gravatar for Joe
10 days ago by
Joe0
Vancouver
Joe0 wrote:

Hi there,

I try to use expression array data (not RNA-sequencing data) to predict ethnicity. Is it possible and any good methods? Many thanks!

Joe

ethnicity expression array • 128 views
ADD COMMENTlink modified 10 days ago by Kevin Blighe13k • written 10 days ago by Joe0

Why did you use the RNA-seq tag for your post if your question is about microarray data?

ADD REPLYlink written 10 days ago by dario.garvan400

Sorry for that. I didn't find the microarray tag.

ADD REPLYlink written 10 days ago by Joe0

I've changed your tags to better reflect your question.

ADD REPLYlink written 10 days ago by Kevin Blighe13k
1
gravatar for dario.garvan
10 days ago by
dario.garvan400
Australia
dario.garvan400 wrote:

It is possible. Any multi-class classification algorithm would be applicable, such as multinomial logistic regression or random forest.

ADD COMMENTlink written 10 days ago by dario.garvan400

Awesome! I will try those algorithms. Thanks for your reply and have a good day.

ADD REPLYlink written 10 days ago by Joe0

Just be careful about the interpretation, as ethnicities are not regarded as having differences at the gene expression level. I feel that you will likely find differences in mitochondrial genes and other genes that are mostly unstudied, like non-coding RNAs. The availability of these transcripts will depend on the array type that you're using, of course.

Ethnic differences at the genetic level, however, are well documented and need no introduction.

ADD REPLYlink written 10 days ago by Kevin Blighe13k
1
gravatar for Shicheng Guo
10 days ago by
Shicheng Guo4.6k
Shicheng Guo4.6k wrote:

Method is not the key problem. The main problem is that it is hard to find the data to train the model. Another problem is I am thinking it will be quite hard to distinguish ethnicity with expression array data.

ADD COMMENTlink written 10 days ago by Shicheng Guo4.6k

That was my first thought, too, upon reading this post. Different ethnicities are not regarded as differing based on gene expression. You may find ethnic-specific expression differences in a disease situation, though

ADD REPLYlink written 10 days ago by Kevin Blighe13k
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