Entering edit mode
8.1 years ago
hAjmal
▴
50
Hi All, How to see if the genes are up or down regulated in the publicly available dataset GDS4296 which contains analysis from cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, and Renal) from the NCI-60 panel? Regards
Have you tried the GEO2R option available from within GEO? That a quick and easy method that tends to work well enough.
Yes I have looked into that, but what I dont understand is what will be the control(no cancer) group?
Control is the group of samples, with which you will have to compare the patient samples. For each tissue, there should be different controls.
Thats where I find it confusing. I want to analyze this GEO dataset with levels in non cancerous samples. I dont know which ones are the control (non cancer) samples, if any
Can you mention the GEO ID?
The acession number is GEO GDS4296
The cancer panel doesn't have controls with it. You can only look at differences between cell types.
Thanks. I have moved to another dataset "GSE62944"