Search

Clear search

Close search

Main menu

Google apps

Genomic SEM Users

Contact owners and managers

1–30 of 310

Welcome to the Genomic SEM Users google group! You can use this page to post questions about the package, bugs/errors you are experiencing, and feature requests.

0 selected

John Meredith, … Aoife3

Apr 10

Runtime differences between models

Thanks for asking this. I am also interested in this answer. Best, Aoife On Wednesday, April 2, 2025

unread,

Runtime differences between models

Thanks for asking this. I am also interested in this answer. Best, Aoife On Wednesday, April 2, 2025

Apr 10

Liam Veltman, … Elliot Tucker-Drob4

Apr 7

Latent factor with 2 Indicators

When fixing two loadings to be equal, you still need the usual constraint to identify the scale of

unread,

Latent factor with 2 Indicators

When fixing two loadings to be equal, you still need the usual constraint to identify the scale of

Apr 7

Patricia Pombo Segura, Thanh Le3

Apr 2

lavaan warning Model estimation FAILED - userGWAS

Hi Thanh Le, We actually modified the model used for userGWAS() and, while the warning still appears

unread,

lavaan warning Model estimation FAILED - userGWAS

Hi Thanh Le, We actually modified the model used for userGWAS() and, while the warning still appears

Apr 2

Morgan Morgan, Elliot Tucker-Drob2

Mar 28

Does usermodel fix residual variances to aid in identification?

I see that the std_genotype estimates are where you are observing the strange behavior (residual

unread,

Does usermodel fix residual variances to aid in identification?

I see that the std_genotype estimates are where you are observing the strange behavior (residual

Mar 28

Mar 26

Continued execution of userGWAS() even with bad SNPs

I forgot to mention the error I encountered. It is ""Error message: task 1 failed - \"

unread,

Continued execution of userGWAS() even with bad SNPs

I forgot to mention the error I encountered. It is ""Error message: task 1 failed - \"

Mar 26

Mar 25

userGWAS () - Running time very slow and cluster computer required?

Hi, I am running GSEM analyses where I am trying to follow the same methodology as the "

unread,

userGWAS () - Running time very slow and cluster computer required?

Hi, I am running GSEM analyses where I am trying to follow the same methodology as the "

Mar 25

güneş can, Elliot Tucker-Drob2

Mar 22

Please see yesterday's thread and search the google group for “two indicators” (also search “2

unread,

Please see yesterday's thread and search the google group for “two indicators” (also search “2

Mar 22

Dúalta McGrath, Elliot Tucker-Drob2

Mar 21

Singularity error comonfactorGWAS

it seems that you are trying to fit a factor model with only two indicators. such a model is not

unread,

Singularity error comonfactorGWAS

it seems that you are trying to fit a factor model with only two indicators. such a model is not

Mar 21

Mar 4

Generating EAF from GWAS results

Hi all: I have generated GWAS result using GenomicSEM with MAF from provided reference file. However,

unread,

Generating EAF from GWAS results

Hi all: I have generated GWAS result using GenomicSEM with MAF from provided reference file. However,

Mar 4

Royce Clifford, Elliot Tucker-Drob4

Mar 1

Finding Neff with only P-value, Odds Ratio, and individual frequencies in a meta-analysis

For my LDSC calculations, I'm getting crazy Total h2 liabilities for individual cohorts, crazy

unread,

Finding Neff with only P-value, Odds Ratio, and individual frequencies in a meta-analysis

For my LDSC calculations, I'm getting crazy Total h2 liabilities for individual cohorts, crazy

Mar 1

Mingyi Du, Michel Nivard2

Feb 12

Re: Low Neff and mean chi^2 for latent factor in a hierarchical model

Hi Mingyi, Can you provide the model fi/results for the factor model without the SNP for us? What

unread,

Re: Low Neff and mean chi^2 for latent factor in a hierarchical model

Hi Mingyi, Can you provide the model fi/results for the factor model without the SNP for us? What

Feb 12

GenEpiLab, Elliot Tucker-Drob2

Feb 9

SNP effects on the residual (unique) variance

Such a model is not identified but the Qsnp statistic will be very useful here and you can perform

unread,

SNP effects on the residual (unique) variance

Such a model is not identified but the Qsnp statistic will be very useful here and you can perform

Feb 9

Elliot Tucker-Drob3

Feb 7

Re: [GenomicSEM/GenomicSEM] Question about implied sample size (Issue #100)

you're asking me to make backwards inference about what model you fit and what your parameter

unread,

Re: [GenomicSEM/GenomicSEM] Question about implied sample size (Issue #100)

you're asking me to make backwards inference about what model you fit and what your parameter

Feb 7

Tomas Gomes, Elliot Tucker-Drob2

Feb 6

NEFF Calculations and Relatedness Clarifications

Neff_hat, ie inferred from betas and SEs is the way to go in that sort of situation. We provide

unread,

NEFF Calculations and Relatedness Clarifications

Neff_hat, ie inferred from betas and SEs is the way to go in that sort of situation. We provide

Feb 6

Pashupati Mishra

Jan 13

LD scores and HM3 reference file based on GRCh38

Hi, I was wondering if the EUR LD score data and HM3 reference files also available with GRCh38 build

unread,

LD scores and HM3 reference file based on GRCh38

Hi, I was wondering if the EUR LD score data and HM3 reference files also available with GRCh38 build

Jan 13

Merli Koitmäe, agro...@gmail.com6

12/30/24

QSNP and corresponding pvalues NA

Dear Andrew, They updated GenomicSEM in server, I reran the analysis on some SNPs, but the Q_SNP

unread,

QSNP and corresponding pvalues NA

Dear Andrew, They updated GenomicSEM in server, I reran the analysis on some SNPs, but the Q_SNP

12/30/24

Thanh Le, … Elliot Tucker-Drob3

12/9/24

NaN for estimated SE (both unstandardized and standardized)

It looks like F3 is a higher order factor with two indicators. A two indicator factor is not

unread,

NaN for estimated SE (both unstandardized and standardized)

It looks like F3 is a higher order factor with two indicators. A two indicator factor is not

12/9/24

John Meredith, … Michel Nivard6

12/5/24

userGWAS Error in eigen(V_full) : infinite or missing values in 'x'

Does anyone have any insight on what may be causing these problems or have brainstorming ideas for

unread,

userGWAS Error in eigen(V_full) : infinite or missing values in 'x'

Does anyone have any insight on what may be causing these problems or have brainstorming ideas for

12/5/24

lydia li, Elliot Tucker-Drob5

11/29/24

calculate effective sample size per SNP

In that case you can use the standard liability threshold model and simply enter the relevant

unread,

calculate effective sample size per SNP

In that case you can use the standard liability threshold model and simply enter the relevant

11/29/24

11/29/24

Model without SNP effects is not identified (df=18) while being identified with SNP effects

Hello everyone, Using 8 traits, I arrived at a hierarchical model with a good fit of CFI being

unread,

Model without SNP effects is not identified (df=18) while being identified with SNP effects

Hello everyone, Using 8 traits, I arrived at a hierarchical model with a good fit of CFI being

11/29/24

Lindsay Melhuish Beaupre

11/26/24

GWAS by subtraction tutorial warning with sumstats command

Hi, I get the following error when I run the sumstats portion of the gwas by subtraction tutorial:

unread,

GWAS by subtraction tutorial warning with sumstats command

Hi, I get the following error when I run the sumstats portion of the gwas by subtraction tutorial:

11/26/24

Matthew Yao, agro...@gmail.com2

11/26/24

Error in nrow(SNPs2) : object 'SNPs2' not found

Hi Matthew, This should be fixed now if you restart and reinstall the package. Best, Andrew On

unread,

Error in nrow(SNPs2) : object 'SNPs2' not found

Hi Matthew, This should be fixed now if you restart and reinstall the package. Best, Andrew On

11/26/24

mike, … agro...@gmail.com4

11/26/24

object 'SNPs2' not found

Hi Matthew, This should be fixed now if you restart and reinstall the package. Best, Andrew On

unread,

object 'SNPs2' not found

Hi Matthew, This should be fixed now if you restart and reinstall the package. Best, Andrew On

11/26/24

Maryam Kazemi, agro...@gmail.com2

11/11/24

LDSC step error

Hi Maryam, The traits listed in the LDSC step should be the munged files (with the .sumstats.gz file

unread,

LDSC step error

Hi Maryam, The traits listed in the LDSC step should be the munged files (with the .sumstats.gz file

11/11/24

Renata Cupertino, … John Meredith6

11/1/24

multivariate GWAS using GenomicSEM - sumstats function

It looks like this worked! Thank you very much for the quick response. Best, John On Friday, November

unread,

multivariate GWAS using GenomicSEM - sumstats function

It looks like this worked! Thank you very much for the quick response. Best, John On Friday, November

11/1/24

Pashupati Mishra, agro...@gmail.com2

11/1/24

Runtime for multivariate GWAS with large number of traits and SNPs

Hi Pashupati, There are two main things you can to do when you have that many SNPs: 1. The estimated

unread,

Runtime for multivariate GWAS with large number of traits and SNPs

Hi Pashupati, There are two main things you can to do when you have that many SNPs: 1. The estimated

11/1/24

Thanh Le, agro...@gmail.com2

11/1/24

userGWAS: warning "some estimated ov variances are negative", NA Qsnp

Hi Thanh Le, Thanks for raising this! The new way of calculating factor-specific Qsnp uses as part of

unread,

userGWAS: warning "some estimated ov variances are negative", NA Qsnp

Hi Thanh Le, Thanks for raising this! The new way of calculating factor-specific Qsnp uses as part of

11/1/24

Joëlle Pasman, … Michel Nivard6

10/8/24

Change in usermodel breaks models that previously ran without issues

Great to hear Joelle, I think this isn't a model you build a paper around but rather a model you

unread,

Change in usermodel breaks models that previously ran without issues

Great to hear Joelle, I think this isn't a model you build a paper around but rather a model you

10/8/24

Maryam Nasserinejad, agro...@gmail.com4

9/25/24

Error in Munge Function: Duplicate Row Names and Embedded Nulls in Summary Statistics

Hi Maryam, It looks like this issue arises only when you use the .gz files as input. Once I unzip

unread,

Error in Munge Function: Duplicate Row Names and Embedded Nulls in Summary Statistics

Hi Maryam, It looks like this issue arises only when you use the .gz files as input. Once I unzip

9/25/24

Apurva Chitre, … Elliot Tucker-Drob7

9/24/24

Genomic SEM v0.0.5 commonfactor() Singular Error with HS Rat Data

Hi Apurva, While I'm not familiar with standard practices in this area of research, I should say

unread,

Genomic SEM v0.0.5 commonfactor() Singular Error with HS Rat Data

Hi Apurva, While I'm not familiar with standard practices in this area of research, I should say

9/24/24