Hi everyone,
I am working with data obtained from the Geo (NCBI). This data is gene expression found with the Affymetrix Human Genome U133A Array and is analysed to get a log2 from the raw data (fastlo normalized, rma summarized). Could you help me understand what this data is and how should I plot it? I thought that I should just plot it normally, but my PI tells me it is possible that I should put it in a logarithmic scale.
Thank you for your help.
It is the question, what you want to see: It is not useful to show all > 20000 RMA normalized expression values. You could reduce the number of genes to the significant differently expressed ones. You could calculate a Volcano plot (or Limma Volcano plot). With reduced expression values you could create hierarchical cluster figures and so on. There are a lot of possibilities, but you have to do some calculations before.
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