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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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Sep 1

Error in factanel

Hey I am trying to run an EFA with 6 factors and 77 traits. Here is my script: EFA_6<-factanal(

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Error in factanel

Hey I am trying to run an EFA with 6 factors and 77 traits. Here is my script: EFA_6<-factanal(

Sep 1

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

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

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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 8

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

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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 8

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

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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

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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

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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

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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

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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

12/4/24

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

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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

12/4/24

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

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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

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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

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