Question regarding input

[Jack McNamara]

Hello, 

For a GEO dataset we are interested in analyzing (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39477), I see the values reported for each patient is the log ratio of expression for a given gene in lymphedema to that expression in a control. 

I do not know if this input would be compatible with GSEA, but wanted to reach out to ask. 

Thank you in advance for your help, 

Jack McNamara

[Anthony Castanza]

Hi Jack,

 

The “log2_lymphedema-vs-normal_ratios” data should be reasonable to use with GSEA Preranked. The identifiers appear to be in Probe IDs, so based on the GEO record, the correct chip would be Human_AGILENT_Array

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Jack McNamara]

Great, thank you very much!

Jack McNamara 

Robert Wood Johnson Medical School 

2LT, United States Army, Medical Corps 

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