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GSVA Enrichment score and correlation

Hi,

I am working on a RNAseq dataset and I was asked to calculate the enrichment score(ES) (GSVA) of a cohort of 24 samples separated in 4 groups over 3 different days (day0,day3,day7). The next step is to correlate these scores with later (day10-Day63) readouts ( cellular responses, humoral reponses). I managed to calculate the ES and calculated a correlation between the ES of a single day with the value of all other days. But then my boss asked me to do a ratio between the scores of day3/day0 Day7/Day0 Day7/Day3 to add a component of time in our scores but I don't feel like it makes any sense. Could anybody help me with this, I feel like we are doing something wrong.

example of what I have done

Thank you for the help

rna-seq gsva r
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written by loicborcard01 • loicborcard01

Not entirely sure what is the issue. If you have a question about your supervisor's idea, then raise it with them.

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written by Kevin Blighe Kevin Blighe

My question is: is it legitimate to do a ratio between the 2 ES and loose the sign (+/-) of my ES in the porcess and then use this value to calculate a pearson correlation ? On top of that the distribution of the ES score looks weird after this opperation.

And second question would be: is there any other way to go about this project ? sorry if it is not clear I am new to this and I am not sure of what I am doing. Another question is : would it make sense to use the ES of a single day to do the correlation without doing the ratio with Day0 (day3/day0).?

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written by loicborcard01 • loicborcard01

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