Closed resztak closed 4 years ago
@resztak are the input summary data also zero for betahat and sebetahat values -- could you verify that is not the case?
> summary(data$Bhat)
Tcell_CTRL Tcell_PHA.EtOH
Min. :-0.882812 Min. :-1.0828800
1st Qu.:-0.072281 1st Qu.:-0.0893518
Median : 0.003624 Median :-0.0000078
Mean : 0.003505 Mean :-0.0003451
3rd Qu.: 0.080291 3rd Qu.: 0.0894630
Max. : 0.784327 Max. : 1.0646300
> summary(data$Shat)
Tcell_CTRL Tcell_PHA.EtOH
Min. :0.1366 Min. :0.1357
1st Qu.:0.3099 1st Qu.:0.3250
Median :0.3624 Median :0.3973
Mean :0.3514 Mean :0.3829
3rd Qu.:0.4017 3rd Qu.:0.4451
Max. :0.6692 Max. :0.7237
@resztak Plotting the z-scores, at first glance it looks very much like "null" data:
load("mashr_chr10_sample_data.Rd")
slopes <- as.matrix(slopes)
SEs <- as.matrix(SEs)
hist(slopes/SEs,n = 100)
Maybe chr10 is not representative..? This is a QQplot for all tests for one of the conditions in the example. I'll investigate on my end.
@pcarbo I think we may have a problem on how we try to get the SE. fastQTL wasn't providing them, and we calculated them manually, and we may have done something wrong. I will go over this with Justyna.
Okay, so rpique was right - we calculated the SE wrong (it was sqrt of SE instead) :sweat_smile: Now I'm getting mean, sd and lfsr estimates from mash (some significant). Sorry I have bothered you!
I'm running mash on FastQTL eQTL mapping results (chr10 for simplicity) following the workflow at https://stephenslab.github.io/mashr/articles/intro_mash.html but no matter if I'm using canonical or data-driven covariance matrices (or both), I get all posterior mean and SD equal to 0 (and all local false sign rate = 1). Here's my code and preprocessed input data (removed all lines with any NAs/Inf) for two conditions: http://genome.grid.wayne.edu/SCAIP_mashr_github/