median value issue for munge_sumstats.py

[argossy]

I have problem using munge_sumstats.py for one of gwas data, I used the effect size as the summary statistics, the errors shows below:

Traceback (most recent call last): File "/nas02/home/k/x/kxia/software/ldsc/munge_sumstats.py", line 654, in munge_sumstats check_median(dat.SIGNED_SUMSTAT, signed_sumstat_null, 0.1, sign_cname)) File "/nas02/home/k/x/kxia/software/ldsc/munge_sumstats.py", line 366, in check_median raise ValueError(msg.format(F=name, M=expected_median, V=round(m, 2))) ValueError: WARNING: median value of SIGNED_SUMSTATS is 2.2 (should be close to 0.0). This column may be mislabeled.

Any method to fix this? Thank you

[bneale]

Hi

The median of your summary statistics is near 2.2 - is this a GWAS? Can you provide a little more context on what the summary statistics are?

Best, Ben

On Thu, Oct 22, 2015 at 10:42 AM, argossy notifications@github.com wrote:

I have problem using munge_sumstats.py for one of gwas data, I used the effect size as the summary statistics, the errors shows below:

Traceback (most recent call last): File "/nas02/home/k/x/kxia/software/ldsc/munge_sumstats.py", line 654, in munge_sumstats check_median(dat.SIGNED_SUMSTAT, signed_sumstat_null, 0.1, sign_cname)) File "/nas02/home/k/x/kxia/software/ldsc/munge_sumstats.py", line 366, in check_median raise ValueError(msg.format(F=name, M=expected_median, V=round(m, 2))) ValueError: WARNING: median value of SIGNED_SUMSTATS is 2.2 (should be close to 0.0). This column may be mislabeled.

Any method to fix this? Thank you

— Reply to this email directly or view it on GitHub https://github.com/bulik/ldsc/issues/37.

For scheduling matters, please contact Carla Hammond < hammond@atgu.mgh.harvard.edu>

Benjamin Neale, Ph.D. Assistant Professor Analytic and Translational Genetics Unit Massachusetts General Hospital Institute Member Stanley Center for Psychiatric Disease and Program in Medical and Population Genetics Broad Institute

[argossy]

This is a GWAS data imputed to 1000G. the summary statistics is effect size. Please let me know if you need further information. Thank you

[bneale]

Can you plot the distribution of effect sizes? What kind of association test are you performing and what phenotype?

On Thu, Oct 22, 2015 at 11:02 AM, argossy notifications@github.com wrote:

This is a GWAS data imputed to 1000G. the summary statistics is effect size. Please let me know if you need further information. Thank you

— Reply to this email directly or view it on GitHub https://github.com/bulik/ldsc/issues/37#issuecomment-150254346.

For scheduling matters, please contact Carla Hammond < hammond@atgu.mgh.harvard.edu>

Benjamin Neale, Ph.D. Assistant Professor Analytic and Translational Genetics Unit Massachusetts General Hospital Institute Member Stanley Center for Psychiatric Disease and Program in Medical and Population Genetics Broad Institute

[argossy]

please see the figure attached for the histogram. the association test is linear regression and the phenotype is Intracranial volume of human brai

n

[bneale]

Hi

I see - try dividing by the standard deviation. That should sort out the problem.

Best Ben

On Thursday, October 22, 2015, argossy notifications@github.com wrote:

please see the figure attached for the histogram. the association test is linear regression and the phenotype is Intracranial volume of human brai [image: histogram_effect_size] https://cloud.githubusercontent.com/assets/15249818/10676098/fd93d3aa-78d1-11e5-9154-f4b4167c107d.png

n

— Reply to this email directly or view it on GitHub https://github.com/bulik/ldsc/issues/37#issuecomment-150330930.

For scheduling matters, please contact Carla Hammond < hammond@atgu.mgh.harvard.edu>

Benjamin Neale, Ph.D. Assistant Professor Analytic and Translational Genetics Unit Massachusetts General Hospital Institute Member Stanley Center for Psychiatric Disease and Program in Medical and Population Genetics Broad Institute

[argossy]

Thanks. it works and fixes the issue.