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chrchang
What is the multiple correction method used in CNV region-based assco
Hi Christopher,
I have got some CNV results for about 1000 samples, and I followed the instructions http://zzz.bwh.harvard.edu/plink/cnv.shtml#reg-assoc on the website to perform a region-based association test. In the result there’s a EMP1 and EMP2.
As what it says on the web page, EMP1 Empirical p-value, per region EMP2 Empirical p-value, corrected for all tests
However, it is not very clear to me how EMP2 was calculated, by that I mean what method has been applied for multiple tests correction. Base on my data results, the correction seems to be stringent.
I’ve looked at other sections on the web page but couldn’t find a clear answer.
Could you explain a little on that or please point me to the relevant resources.
Thank you very much.
Regards, Ruqian
Hi,
The results I have got were by plink/1.0.7. I have actually got multiple versions of plink installed on our cluster. I also have access to 1.9.0 and 2.0.0a.
Is it different in terms of the multiple test correction methods?
Regards, Ruqian
2018-01-30 19:44 GMT+11:00 MaggieJJ [email protected]:
hello
do you us plink v1.07 ?
Regards
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Hi,
I see that the CNV analysis is no longer supported by new versions of Plink.
I checked plink/seq too. It does not look like it deals with CNV results, does it?
Thank you
Regards, Ruqian
2018-01-31 9:22 GMT+11:00 Rachel Lyu [email protected]:
Hi,
The results I have got were by plink/1.0.7. I have actually got multiple versions of plink installed on our cluster. I also have access to 1.9.0 and 2.0.0a.
Is it different in terms of the multiple test correction methods?
Regards, Ruqian
2018-01-30 19:44 GMT+11:00 MaggieJJ [email protected]:
hello
do you us plink v1.07 ?
Regards
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Hi,
I also run it by plink v1.0.7, both EMP1 and EMP2 are 1. I am puzzled. My shell is:
plink-1.07-x86_64/plink --cnv-list genomestrip.cnv --map plink.cnv.map --fam genomestrip.fam --cnv-intersect glist-hg38.dms --cnv-test-region --mperm 10000
Regards,