Hi, I am trying to correlate glucose levels (SSPG) and gene expression differences between individuals before (post) and after (pre) meals. In addition, I need to correct it for the protocol (Prep), age, weight differences between post and pre.

I am using the following formula to do it. Could you please let me know if this is a correct way or not?

### head (clinical_data)

                Sample.ID Time.Point Prep Age SSPG weight..kg.
1396-807_pre_L   1396-807        pre    L  51  140      101.97
1396-807_post_L  1396-807       post    L  51  201      105.35
1396-006_pre_B   1396-006        pre    B  52  117       70.00
1396-006_post_B  1396-006       post    B  52  115       72.77
1396-006_pre_L   1396-006        pre    L  52  117       70.00
1396-006_post_L  1396-006       post    L  52  115       72.77

### design matrix
design <- model.matrix(SSPG ~ Time.Point + 
                         Prep + Age + weight..kg., 
                       data=clinical_data)

If you want to correlate SSPG with expression, then you need to include SSPG in the design matrix, just like you've done with Age and weight etc.