Hi. I want to do GSEA on my DE genes comparing sample 1 with sample 2. However, I cant seem to find a way of getting hold of the normalised expression for each gene. Using volcano plot CSV function gives me log fc, p-value, but there is only one average expression column, not one for each sample. Is there a way of getting hold of this data?
The simplest way to download the information that you’re looking for is to use the the new ‘Normalized Expression Matrix’ option in the Plots and Tables module:
You can select which samples, metadata groups and/or clusters you would like to ‘subset’ by prior to downloading the matrix:
This new feature was only released last week so please do let us know your feedback! Does it enable you to download the information that you’re looking for?