The proper order of defining groups in GEO2R

Question

[nazaninhoseinkhan]

Dear all,

I used GEO2R to find the list of differential expressed genes between cancer and normal tissue.

I did not know the expression of which group(cancer or normal) is divided on the other group.

I found a tutorial in which it had been said that the treated group must be defined first (indicated by blue in GEO2R).

However the results that I get is not in agreement with the previously reported up or down-regulation for most of genes.

Can anybody tell me what is the correct order of defining groups in GEO2R?

Thank you in advance

Nazanin

Answer 1

[Leite]

Hi Nazanin,

I think a question similar to that has been answered before.

Look that: > How to define groups in GEO2R tool?

Answer 2

[murshad.60ali]

The order in which you assign the groups is important. First define the treated group (it will be colored in blue), then define the control group (it will be colored in pink). The order is important for calculating log fold changes later in the analysis. If you reverse the order: genes that are upregulated according to the publication that supports the data will be downregulated in your results and vice versa

https://wiki.bits.vib.be/index.php/Analyze_GEO_data_with_GEO2R

Answer 3

[nightmoonshen]

I am also confused by this question