Question: Similarity of sequential samples
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gravatar for skal
4 weeks ago by
skal0
skal0 wrote:

I'm trying to find a way to examine the similarity of sequential samples taken from a patient. Let's say, that I have 10 patients (A, B, C, D etc.) and from each I have three samples taken at different time points (1, 2, 3). I have gene expression data from each sample. Now I would like to find out whether the three samples from each patient are similar. I have done clustering, differential gene expression analysis (paired) and correlation analyses, and I can see that the samples correlate, but there are also differences. Is there a way to determine whether samples 1-3 from a patient are statistically similar to each other? So that similar assumptions can be made based on, for instance, sample 3 (patient A) as from sample 1 (patient A).

similarity R gene • 126 views
ADD COMMENTlink modified 11 days ago by Biostar ♦♦ 20 • written 4 weeks ago by skal0

Isn't it sufficient to take all DEGs, put into hclust and see that samples per patient are closer to each other than to the rest? You don't have to put a pvalue on everything, clustering is perfectly valid to show similarities if you ask me.

ADD REPLYlink written 4 weeks ago by ATpoint40k
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