RNA-seq meta analysis

Question

[zizigolu]

hi,

I am going to do some analysis on brassinosteroid responsive genes in Arabidopsis thaliana

I found these RNA-seq experiments about brassinosteroids in Arabidopsis, do you think if such an arrangement make any sense in meta analysis?

thank you

      plant tissue                    age        day light          treatment    time     control arrays    treated arrays
1     seedling/WT                     7 days     dark for 7 D       BL           4 h      2                 2
2     Root-WT                         7 days     day light          BL           4 h      2                 2
3     root/bri1-116, - mutant         7 days     day light                                2                 2
4     root/bri1-116,bz1-116 mutant    7 days                                              2                 2

[Devon Ryan]

As a general rule, if the different groups were each run at different times or at different places then comparing them is going to lead to questionable results.

[zizigolu]

thank you, the experiments were done in different labs and time. I am too beginner in bioinformatics then if my purpose is not wise I am wasting my time on a difficult process that is why I am hesitate about the workflow