Question: Classification Of Samples Based On Gene Expression Values
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gravatar for Ngsnewbie
6.4 years ago by
Ngsnewbie360
Ngsnewbie360 wrote:

I have 8 samples ( of which 4 are pre treatment and 4 are post treatment ) where the sample names are unknown , means i dont know what samples belongs to pre treatment and what belongs to post treatment. The gene expression values (count value as well as FPKM) are available. So the objective is be divide them into two groups (4 sample each). What are the best approches to classify on the basis of gene expression values. I have tried hierarchical clustering based on euclidean distance but i am not comfortable with the results. I want to know other algorithms, tools or methodology that can serve best for such classification. Thanks.

ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 6.4 years ago by Ngsnewbie360

This is really an open ended question as there are probably a dozen methods of clustering your reads: What is your research question and what is your criteria for comparing your transcripts? I'm a little confused also: you have 4 control and 4 treatment samples; you don't know which ones are which ("sample names are unknown")? What does "these have to be divided into two groups" mean?

ADD REPLYlink written 6.4 years ago by Josh Herr5.6k
1

Yes i dont know which one are which !! , and these 8 have to segregate into two groups pre-treatment and post-treatment. So the query is: I have 8 samples (of which 4 belongs to pre-treatment and 4 belongs to post treatment, but i dont know which sample belongs to which one). So i am finding out the best way to cluster/classify these 8 samples into these two group.

Note: I have edited the language of my question in order to make it comprehensive.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Ngsnewbie360
2

I don't think it's a good idea to label unknown samples based on gene expression clustering. My best suggestion is to start the sequencing over and make sure you know which samples are your control and which samples are your treatment.

ADD REPLYlink written 6.4 years ago by Josh Herr5.6k
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