You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hello, I'm using mashr for my research, and I'm trying to discriminate eQTLs which are same or different among conditions.
I've seen a tutorial from vignette, which uses get_pairwise_sharing_from_samples with an arbitrary cutoff (factor=0.5).
But I'm now trying t-test using posterior mean and standard deviation (sd) values.
I'm doing this with following R codes (for example).
When sample size / posterior mean / posterior sd of an eQTL from condition A are 101 / 0.5 / 0.07,
and those from condition B are 121 / 0.3 / 0.06,
(I'll also do Bonferroni correction)
--->> As a result, eQTLs with adjusted p-values below cutoff will be considered A- or B-dominant eQTLs.
So, my question is,
Is my idea theoretically valid?
Especially I'm a bit confused whether posterior estimates are suitable to become inputs for general t-test.
Could you give me some advice?
The text was updated successfully, but these errors were encountered:
At first, I followed this: https://stephenslab.github.io/mashr/articles/mash_sampling.html
In "Pairwise sharing" chapter, it contains how to compare effects from two conditions, and I understood that mashr uses an arbitrary cutoff for difference of two posterior means to decide condition-specificity of an eQTL.
Instead of the arbitrary cutoff, I'm trying to use t-test to decide whether two posterior means are same or different.
I think this way may solve ambiguity during pairwise comparison of eQTLs.
But I'm not familiar with statistics, so I'm not sure if my idea is valid.
@MaximalLife The statistic you want to compute will depend on what question you are answering. It might help to look at Fig. 5 and the section "Sharing of effects among tissues" in our paper, where we consider two different ways of quantifying sharing of effects across tissues/conditions.
Hello, I'm using mashr for my research, and I'm trying to discriminate eQTLs which are same or different among conditions.
I've seen a tutorial from vignette, which uses
get_pairwise_sharing_from_samples
with an arbitrary cutoff (factor=0.5).But I'm now trying t-test using posterior mean and standard deviation (sd) values.
I'm doing this with following R codes (for example).
When sample size / posterior mean / posterior sd of an eQTL from condition A are 101 / 0.5 / 0.07,
and those from condition B are 121 / 0.3 / 0.06,
(I'll also do Bonferroni correction)
--->> As a result, eQTLs with adjusted p-values below cutoff will be considered A- or B-dominant eQTLs.
So, my question is,
Is my idea theoretically valid?
Especially I'm a bit confused whether posterior estimates are suitable to become inputs for general t-test.
Could you give me some advice?
The text was updated successfully, but these errors were encountered: