Open zzf77 opened 1 year ago
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. 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!
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>
, andpval_<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 thediff_mod_rate_con_vs_test
column, this means thattest
<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.
Hello Yuk Kei,
can you please comment on it? I think @zzf77 has valid point.
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.