Question: Using expression array data to predict ethnicty
0
gravatar for Joe
6 months ago by
Joe10
Vancouver
Joe10 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 • 240 views
ADD COMMENTlink modified 6 months ago by Kevin Blighe25k • written 6 months ago by Joe10

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

ADD REPLYlink written 6 months ago by dario.garvan420

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

ADD REPLYlink written 6 months ago by Joe10

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

ADD REPLYlink written 6 months ago by Kevin Blighe25k
1
gravatar for dario.garvan
6 months ago by
dario.garvan420
Australia
dario.garvan420 wrote:

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

ADD COMMENTlink written 6 months ago by dario.garvan420

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

ADD REPLYlink written 6 months ago by Joe10

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 6 months ago by Kevin Blighe25k
1
gravatar for Shicheng Guo
6 months ago by
Shicheng Guo6.1k
Shicheng Guo6.1k 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 6 months ago by Shicheng Guo6.1k

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 6 months ago by Kevin Blighe25k
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