Clustering of samples based on specific gene sets
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cherlyn.t • 0
@cherlynt-13245
Last seen 20 months ago

Hi,

  I am working on data obtained from microarray data. Could anyone enlighten me on how I can group my samples based on 3 particular gene sets. 

thank you.

microarray differential gene expression gene set analysis clustering • 513 views
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Hi, sorry, but this isn't much of a question as you have the answer there already.. you would cluster samples using just the gene sets your interested in. Which typically means sub-setting the rows just to contain the genes that are the members of the gene sets you are interested in.

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Hi Chris, thank you for your response. I think I could have phrased my question better. I was wondering if I could perform supervised clustering, where I combine all three gene sets (ie, the rows contain genes from all 3 gene sets) and perform clustering. My issue is on how I could ensure that the specified genes are within their respective gene sets when I perform the clustering, as they are not grouped based on expression but molecular hallmarks (or developmental stage). I would like to see how the samples would cluster with all three gene sets in the same dataframe, I am just wondering if this is statistically possible. 

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You could just aggregate the gene set genes by their mean, if that makes sense... Then you would be clustering gene sets instead of genes.

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