How can I get p values for all the positions?

[bhargava-morampalli]

The default result is for most significant position in the RNA but is there an option which I can use to get the p-values for all the positions?

[yuukiiwa]

Hi @bhargava-morampalli,

If you use prefiltering like indicated below, then xpore diffmod only outputs the significants positions according to the threshold:

notes: Pairwise comparison without replicates with default parameter setting.

data:
    KO:
        rep1: ./data/HEK293T-METTL3-KO-rep1/dataprep
    WT:
        rep1: ./data/HEK293T-WT-rep1/dataprep    
    
out: ./out

method:
    prefiltering:
        method: t-test
        threshold: 0.1

If you want the pval_<condition1>_vs_<condition2> for all the positions, you will have to remove the prefiltering in config.yml, which is as follow:

notes: Pairwise comparison without replicates with default parameter setting.

data:
    KO:
        rep1: ./data/HEK293T-METTL3-KO-rep1/dataprep
    WT:
        rep1: ./data/HEK293T-WT-rep1/dataprep    
    
out: ./out

Thanks!

Best wishes, Yuk Kei

[bhargava-morampalli]

Thanks @yuukiiwa

I initially ran the xpore without those filtering options and that was the output I was talking about where there are only a few positions.

I tried again and the result is same. Not all positions are represented in the results.

Is there anything else that I could try?

Thanks.

-Bhargava