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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.

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Goodluck li, Elliot Tucker-Drob3

Nov 8

Dear GenomicSEM development team, hello: I have run multiple times on the same machine and version of R/GenomicSEM/lava The results obtained from the second-order two factor model of usermodel (DWLS) are significantly inconsistent, including the coef

Thank you On Wednesday, November 5, 2025 at 8:58:14 PM UTC+8 tucke...@gmail.com wrote: I suspect that

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Dear GenomicSEM development team, hello: I have run multiple times on the same machine and version of R/GenomicSEM/lava The results obtained from the second-order two factor model of usermodel (DWLS) are significantly inconsistent, including the coef

Thank you On Wednesday, November 5, 2025 at 8:58:14 PM UTC+8 tucke...@gmail.com wrote: I suspect that

Nov 8

Nov 8

Subject: How to compute Q_SNP for a higher-order factor model in GenomicSEM?

Hello GenomicSEM team, My current model is: F1 =~ 1*T1 + T2 + T3 + T4 + T5 F2 =~ 1*T6 + T7 + T8 G =~

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Subject: How to compute Q_SNP for a higher-order factor model in GenomicSEM?

Hello GenomicSEM team, My current model is: F1 =~ 1*T1 + T2 + T3 + T4 + T5 F2 =~ 1*T6 + T7 + T8 G =~

Nov 8

Nov 4

What is the "est" value in userGWAS output?

Hi, Is the "est" (estimated effect) always a standardised beta coefficient in userGWAS()

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What is the "est" value in userGWAS output?

Hi, Is the "est" (estimated effect) always a standardised beta coefficient in userGWAS()

Nov 4

Emily Morbey, … agro...@gmail.com4

Oct 30

Use of 1000 genomes reference file

The reverse: A1 = REF A2 = ALT On Thursday, October 30, 2025 at 5:12:26 AM UTC-6 emily.mo...@gmail.

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Use of 1000 genomes reference file

The reverse: A1 = REF A2 = ALT On Thursday, October 30, 2025 at 5:12:26 AM UTC-6 emily.mo...@gmail.

Oct 30

Maryam Marzban, Elliot Tucker-Drob2

Oct 23

common factor gwas

People have asked about factors with two indicators several times before. If you search through the

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common factor gwas

People have asked about factors with two indicators several times before. If you search through the

Oct 23

Thanh Le, Elliot Tucker-Drob2

Oct 6

Should latent variable variance be set to 1 for downstream analyses?

That depends on exactly what you are using those betas and Ns for. If you set the factor SD to 1,

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Should latent variable variance be set to 1 for downstream analyses?

That depends on exactly what you are using those betas and Ns for. If you set the factor SD to 1,

Oct 6

Hyun Seok Do, Elliot Tucker-Drob2

Oct 2

Estimating Q_SNP in hierarchical model

The code you are looking at is a computationally efficient implementation for estimating Q for factor

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Estimating Q_SNP in hierarchical model

The code you are looking at is a computationally efficient implementation for estimating Q for factor

Oct 2

Sep 28

Error in if (a1 != a2) .LOG("The effect column was determined to be coded as an odds ratio (OR) for the ", : missing value where TRUE/FALSE needed

Good morning: I am using brain volume GWAS summary statistics from Tissink, et al. for GSEM. When I

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Error in if (a1 != a2) .LOG("The effect column was determined to be coded as an odds ratio (OR) for the ", : missing value where TRUE/FALSE needed

Good morning: I am using brain volume GWAS summary statistics from Tissink, et al. for GSEM. When I

Sep 28

Sep 27

how to calculate a MAF from multiple cohorts

This is a wonderful conversation group, very helpful. I have sumstats from 4 cohorts, with a combined

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how to calculate a MAF from multiple cohorts

This is a wonderful conversation group, very helpful. I have sumstats from 4 cohorts, with a combined

Sep 27

Sep 23

Error in factanel

I have resolved the problem. Thanks. On Monday, September 1, 2025 at 12:28:45 AM UTC-4 Daniel Rosoff

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Error in factanel

I have resolved the problem. Thanks. On Monday, September 1, 2025 at 12:28:45 AM UTC-4 Daniel Rosoff

Sep 23

yufeng huang, Elliot Tucker-Drob3

Sep 16

Question on Extending GenomicsSEM for Local Genetic Modeling

Thank you so much for the information. I think this will be a very interesting field. On Tue, Sep 16,

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Question on Extending GenomicsSEM for Local Genetic Modeling

Thank you so much for the information. I think this will be a very interesting field. On Tue, Sep 16,

Sep 16

Marta Ribases, Lars Andreas Rømo Ystaas2

Aug 18

GWAS-by-subtraction sumstats genetic correlation

I have the same problem. I've run a GWAS-by-subtraction successfully, but there is still a

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GWAS-by-subtraction sumstats genetic correlation

I have the same problem. I've run a GWAS-by-subtraction successfully, but there is still a

Aug 18

Apurva Chitre, Elliot Tucker-Drob4

Jul 16

Mega vs common-factor MV-GWAS: expected -log10 P difference? (HS rats)

Ahh great. In that case that specification should be appropriate as you have described. By mega scan

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Mega vs common-factor MV-GWAS: expected -log10 P difference? (HS rats)

Ahh great. In that case that specification should be appropriate as you have described. By mega scan

Jul 16

B, Elliot Tucker-Drob3

Jul 11

GenomicSEM: model fit and Residual Covariance Matrix

Dear Elliot Tucker-Drob Thank you very much for your suggestion and input. I will examine the

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GenomicSEM: model fit and Residual Covariance Matrix

Dear Elliot Tucker-Drob Thank you very much for your suggestion and input. I will examine the

Jul 11

Lora Pless, … James Hart3

Jul 11

Hi all, The LD score files linked here by Dr. Grotzinger will work with the ldsc() function after

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Hi all, The LD score files linked here by Dr. Grotzinger will work with the ldsc() function after

Jul 11

Jul 9

standardized or unstandardized different p-value

Hi, I'm estimating the correlation between “trait” and three different latent factors, F_unique,

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standardized or unstandardized different p-value

Hi, I'm estimating the correlation between “trait” and three different latent factors, F_unique,

Jul 9

Jun 4

Usermodel: some estimated ov variances are negative

My model fit: chisq df p_chisq AIC CFI SRMR df 117.4064 42 4.657872e-09 165.4064 0.9851008 0.06495223

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Usermodel: some estimated ov variances are negative

My model fit: chisq df p_chisq AIC CFI SRMR df 117.4064 42 4.657872e-09 165.4064 0.9851008 0.06495223

Jun 4

Elliot Tucker-Drob

May 19

Re: [GenomicSEM/GenomicSEM] How to download full reference set (Issue #109)

It's linked to in the wiki under 5. Multivariate GWAS On Mon, May 19, 2025 at 6:26 PM

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Re: [GenomicSEM/GenomicSEM] How to download full reference set (Issue #109)

It's linked to in the wiki under 5. Multivariate GWAS On Mon, May 19, 2025 at 6:26 PM

May 19

ahmad valikhani, Elliot Tucker-Drob4

May 15

Including Genetic PCA Components in SEM

This group is for the Genomic SEM analytic framework and software, as introduced in this paper:

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Including Genetic PCA Components in SEM

This group is for the Genomic SEM analytic framework and software, as introduced in this paper:

May 15

ahmad valikhani, Elliot Tucker-Drob6

Apr 23

Creating a latent polygenic risk score from two PRSs using SEM

we're getting pretty far afield from Genomic SEM at this point. but you can certainly put two

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Creating a latent polygenic risk score from two PRSs using SEM

we're getting pretty far afield from Genomic SEM at this point. but you can certainly put two

Apr 23

Austin Park, … B4

Apr 15

Standardized factor loading larger than 1

Dear all, Thank you for posting this question and information. I wanted to follow-up on a similar

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Standardized factor loading larger than 1

Dear all, Thank you for posting this question and information. I wanted to follow-up on a similar

Apr 15

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

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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

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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

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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

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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 - \"

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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

güneş can, Elliot Tucker-Drob2

Mar 22

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

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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

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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,

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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

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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

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