Post by Ari Cilleros on Jun 9, 2020 8:45:48 GMT
Hi all,
I am currently trying to run SMR, but I have a small sample size. I saw in the main page of the software that on case of having a small number of samples:
We only store effect size (b) and SE in the BESD file, and re-calculate p-value for analysis when necessary, assuming b / SE follows a standard normal distribution, i.e. N(0, 1). Strictly speaking, b / SE follows a t-distribution which is approximately N(0, 1) if sample size is large. For data sets with small sample sizes (e.g. GTEx), this might lead to a bias in p-value. In this scenario, we recommend users to compute z* based on the original p-value from a standard normal distribution, and adjust the standard error as SE = b / z*. This adjustment guarantees that the re-computed p-value from b and SE being exact the same as the original p-value.
BESD format. (n.d.) Retrieved from cnsgenomics.com/software/smr/#BESDformat
But I don't found any example where it is done or how it is done. I tried to see if there is any flag in SMR documentation that allows me to do this, but I didn't found any.
Thank you so much for your help in advance!
Ari.
I am currently trying to run SMR, but I have a small sample size. I saw in the main page of the software that on case of having a small number of samples:
We only store effect size (b) and SE in the BESD file, and re-calculate p-value for analysis when necessary, assuming b / SE follows a standard normal distribution, i.e. N(0, 1). Strictly speaking, b / SE follows a t-distribution which is approximately N(0, 1) if sample size is large. For data sets with small sample sizes (e.g. GTEx), this might lead to a bias in p-value. In this scenario, we recommend users to compute z* based on the original p-value from a standard normal distribution, and adjust the standard error as SE = b / z*. This adjustment guarantees that the re-computed p-value from b and SE being exact the same as the original p-value.
BESD format. (n.d.) Retrieved from cnsgenomics.com/software/smr/#BESDformat
But I don't found any example where it is done or how it is done. I tried to see if there is any flag in SMR documentation that allows me to do this, but I didn't found any.
Thank you so much for your help in advance!
Ari.