Question: How to find number of patients (percentage of given population) having high expression of gene A in given microarray data ?
gravatar for yuvanesh
13 months ago by
yuvanesh0 wrote:

I have a microarray gene expression data from GEO and I would like to find how many samples has high expression of Gene A.

This is the method that I am following currently

1) Download raw cel file 2) Use rma package to normalize 3) Perform clustering using heatmap based on Gene A 4) By looking at cluster from heatmap, I pick the samples that has highly expressed, low expressed, intermediate expressed of gene A.

1) Is there any other method to identify % of samples that has highly expressed Gene A in the given dataset?

2) How to answer the same question using datasets from multiple studies?

Example: If I have 10 studies from GEO, and all are microarray data,

a) should I perform my clustering individually on each dataset and find % of samples from each study and take an average or?

b) Should I merge dataset using Combat or Limma and then perform clustering to find % of samples that has gene A that are highly expressed?

clustering microarray R gene • 366 views
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