Interpretation of results

[zzf77]

Hi developer,
I have successfully run my data with xpore. But I have a question, how could I distinguish which group has a higher m6A level in a single m6A motif, depending on the diff_mod_rate_con_vs_test? If I got a negitvae number in the diff_mod_rate_con_vs_test column, does it mean the m6A level of the control group at this site is lower than that of the test group? Thank you for your time!
Best wishes.

[yuukiiwa]

Hi @zzf77,

To distinguish which group having a higher m6A level in a single m6A motif, you can look into the diff_mod_rate_<condition1>_vs_<condition2>, z_score_<condition1>_vs_<condition2>, and pval_<condition1>_vs_<condition2> columns.

The direction (either negative or positive) of diff_mod_rate_con_vs_test is alphabetically ordered. If you get a negative number in the diff_mod_rate_con_vs_test column, this means that test < con, which means the site is modified.

Thanks!

Best wishes,
Yuk Kei

[kwonej0617]

Hi, Yuk Kei.
I have a question regarding this from your previous comment, 'If you get a negative number in the diff_mod_rate_con_vs_test column, this means that test < con, which means the site is modified.'.

Isn't diff_mod_rate_con_vs_test column what we would get from mod_rate_con (control, KO, unmodified) - mod_rate_test (WT, modified)? If so, if we get a negative number in the diff_mod_rate_con_vs_test, I think that mod_rate_test (WT, modified) should be greater than mod_rate_con (control, KO, unmodified). Also, when mod_rate_test (WT, modified) is grater than mod_rate_con (control, KO, unmodified), the site is likely to be modified.
Could you please let me know if there's any misunderstanding?

Thank you so much!

[zzf77]

Hi @zzf77,

To distinguish which group having a higher m6A level in a single m6A motif, you can look into the diff_mod_rate_<condition1>_vs_<condition2>, z_score_<condition1>_vs_<condition2>, and pval_<condition1>_vs_<condition2> columns.

The direction (either negative or positive) of diff_mod_rate_con_vs_test is alphabetically ordered. If you get a negative number in the diff_mod_rate_con_vs_test column, this means that test < con, which means the site is modified.

Thanks!

Best wishes, Yuk Kei

Hi, Yuk Kei.
Thank you for your reply! If I got a negative number in the diff_mod_rate_con_vs_test column, this means that test < con, which means the site is modified.
Does it means in this situation the m6A level of test < m6A level of con? If so, the positive number in the diff_mod_rate_con_vs_test column means the m6A level of test > m6A level of con?

Thanks!
Best wishes.

[vetmohit89]

Hello Yuk Kei,

can you please comment on it? I think @zzf77 has valid point.

[g-s-2018]

Hello Yuk Kei,

What is the positive number in the diff_mod_rate_con_vs_test indicate? why do we get the modification rate in two directions?
Thanks in advance