When doing micro-array data analysis for DEG using GEO2R, we are defining groups as test or control for Top 250. Which one to define first? Control or Test? logFC value changes + and - if i choose alternatively. Which one is correct? I used the dataset accession: GSE527 (Normal Cervix as Control & Cervical Cancer as Test).
Control first, test second. I don't have a reference for that but I wrote it down in my notes. Edit: you can have a look at the R code produced from your selection and see how the factor is defined, then check how limma treats the factor.
It doesn't matter which one is define first or second. It neither doesn't matter define which one is case or control. The only thing matters is how to interpret the result. Take your example: in the left frame, + indicate higher in control while in the right frame, - indicate higher in control. Asaf is right you should learn R and try to get the code from GEO2R and try to download and analysis the data more complicated. Don't use GEO2R all the time.
You always want to compare your treatment versus the control and have everything relative to that.
https://wiki.bits.vib.be/index.php/Analyze_GEO_data_with_GEO2R
treatment first then control
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