How group PSIs in effect_sizes.txt are calculated?

[smshuai]

Hello,

I am wondering how PSIs reported in effect_sizes.txt are calculated for each group?

In my understanding, this is the mean intron ratios per cluster per group. However, I did calculation myself based on perind_numers.counts.gz but the value is different from what's in effect_sizes.txt.

As an example, for a cluster with 4 introns, PSI for intron3 reported by leafcutter for groupA is 0.648. The count matrix looks like:

   Sample1 Sample2 Sample3 Sample4 Sample5 Sample6
1:       0       0       0       0       0       0
2:       0       1       6       0       0       1
3:      11      40       0       1       0     176
4:       0       0       7       0       0       0

Thus intron ratios for intron3 is like:

3: 1.00 0.98 0.00 1.00 0.97 0.99

The mean ratio is then 0.98498 (my understanding of group PSI).

Can you point out what's my misunderstanding here? Thanks in advance!

[shixianhu]

Hello,

I am wondering how PSIs reported in effect_sizes.txt are calculated for each group?

In my understanding, this is the mean intron ratios per cluster per group. However, I did calculation myself based on perind_numers.counts.gz but the value is different from what's in effect_sizes.txt.

As an example, for a cluster with 4 introns, PSI for intron3 reported by leafcutter for groupA is 0.648. The count matrix looks like:

   Sample1 Sample2 Sample3 Sample4 Sample5 Sample6
1:       0       0       0       0       0       0
2:       0       1       6       0       0       1
3:      11      40       0       1       0     176
4:       0       0       7       0       0       0

Thus intron ratios for intron3 is like:

3: 1.00 0.98 0.00 1.00 0.97 0.99

The mean ratio is then 0.98498 (my understanding of group PSI).

Can you point out what's my misunderstanding here? Thanks in advance!

Have you solved this, my friend? I cannot repeat the effect size neither. I must miss something, e.g. normalization. Thanks!