question about interpreting the NA value in the mod rate column

[lyj95618]

Hi,

I have three replicates of treated and WT for comparison. In the final result table, I see that in some sites, only one of the replicates has a mod rate reported while the other two have NA in the mod rate column. I am wondering how should I interpret the NA value here. Does that mean there is no modification for those two replicates in this site or xpore just didn't detect anything at this site?

Is the diff_mod_rate_conditionA_vs_conditionB still meaningful if only one of the replicates in the treated and WT has an actual value in the mod rate column?

Thanks for the help!
Laur

[yuukiiwa]

Hi @lyj95618,

Sorry for the delayed reply!

You have three replicates, and for one site, you have three mod_rates for the three replicates, where two of them are NAs. This could be that this site shows up only in one replicate but not the other two (could be due to upstream sequencing quality discrepancy).

On our end, we have done analyses using only one replicate for the two groups, so you can see whether the one replicate analysis is good enough for you.

Thanks!

Best wishes,
Yuk Kei

[lyj95618]

@yuukiiwa Thank you very much for your reply!

If possible, could you please point me to the paper or link where those analyses are? Is it in the Xpore paper? I am interested in knowing what I can do with those data since a lot of sites only have one mod_rate available.

Thank you so much for your help!
Laur

[yuukiiwa]

Hi Laur (tagging you here @lyj95618),

For the xpore paper, we did it on 3 replicates, but we have confidential analyses done on 1 replicate only.

With one replicate for each sample, you can still use the z-score to infer whether sites from the two samples are differentially modified.

Thanks!

Best wishes,
Yuk Kei