# ISG Workshop 2026 **URL:** https://isgw-forum.colorado.edu/c/isg-workshops-2026/28.md?page=1 [Latest](https://isgw-forum.colorado.edu/latest.md) · [Categories](https://isgw-forum.colorado.edu/categories.md) · [Tags](https://isgw-forum.colorado.edu/tags.md) **Page:** 2 --- ## [Identifying Latent Variables](https://isgw-forum.colorado.edu/t/identifying-latent-variables/889)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:27pm UTC](https://isgw-forum.colorado.edu/t/identifying-latent-variables/889 "2026-06-10T14:27:15Z")
In the slides for today, variance for latent factors was fixed to 1 to make them identified. On Hermine’s day, the twin model fixed coefficients to 1 instead of variances to 1. In general, how do people decide what to f… --- ## [S Matrix, Genetic Correlations, and Twin Models](https://isgw-forum.colorado.edu/t/s-matrix-genetic-correlations-and-twin-models/888)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:26pm UTC](https://isgw-forum.colorado.edu/t/s-matrix-genetic-correlations-and-twin-models/888 "2026-06-10T14:26:19Z")
Is genetic correlation (off diagnonal values in the S matrix) more similar to bh2 (bivariate heritability) or rg (genetic correlations) in the bivariate twin models? Replying to “Is genetic correlation (off diagnonal v… --- ## [Latent Variables vs Latent Factors](https://isgw-forum.colorado.edu/t/latent-variables-vs-latent-factors/886)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:25pm UTC](https://isgw-forum.colorado.edu/t/latent-variables-vs-latent-factors/886 "2026-06-10T14:25:48Z")
Is there a difference between a “latent variable” and a “latent factor”? (Both terms were used in today’s slides, but I’m not sure if they’re synonymous or if maybe factor means something special.) Replying to “Is the… --- ## [Comparing LDSC, GREML, and HE Heritability](https://isgw-forum.colorado.edu/t/comparing-ldsc-greml-and-he-heritability/884)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:24pm UTC](https://isgw-forum.colorado.edu/t/comparing-ldsc-greml-and-he-heritability/884 "2026-06-10T14:24:58Z")
Should we check if h2 from sum stats via LDSC are the same/similar to h2 from HE regression/GREML? Replying to “Should we check if h2 from sum stats via LDSC are …”: If you have access to suitable data to check that,… --- ## [Leave-One-Out GWAS for PRS](https://isgw-forum.colorado.edu/t/leave-one-out-gwas-for-prs/882)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:16pm UTC](https://isgw-forum.colorado.edu/t/leave-one-out-gwas-for-prs/882 "2026-06-10T14:16:27Z")
If one wanted to use the five psychiatric latent factors from the Nature paper for PRS analyses, and the cohort of interest contributed to the discovery GWASs used to derive these factors, would it be possible to obtain … --- ## [QSNP Interpretation](https://isgw-forum.colorado.edu/t/qsnp-interpretation/881)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:15pm UTC](https://isgw-forum.colorado.edu/t/qsnp-interpretation/881 "2026-06-10T14:15:53Z")
After identifying all snps with a significant Qsnp for a factor, is it possible to determine which individual phenotypes within that factor are associated with these SNPs? Replying to “After identifying all snps with a… --- ## [userGWAS Matrix Error](https://isgw-forum.colorado.edu/t/usergwas-matrix-error/880)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:15pm UTC](https://isgw-forum.colorado.edu/t/usergwas-matrix-error/880 "2026-06-10T14:15:14Z")
This is a very specific question, but I’ve gotten the error “Error in crossprod(wls.diff, wls.v) : non-conformable arguments Calls: userGWAS”, when running an African-ancestry multivariate gwas. I haven’t been able to fi… --- ## [Running Genomic SEM Locally](https://isgw-forum.colorado.edu/t/running-genomic-sem-locally/879)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:14pm UTC](https://isgw-forum.colorado.edu/t/running-genomic-sem-locally/879 "2026-06-10T14:14:09Z")
meaning we can’t run this locally on our computers? Replying to “meaning we can’t run this locally on our computers…”: with the new version you will be able to Replying to “meaning we can’t run this locally on our … --- ## [Parallel Processing Problems](https://isgw-forum.colorado.edu/t/parallel-processing-problems/878)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:13pm UTC](https://isgw-forum.colorado.edu/t/parallel-processing-problems/878 "2026-06-10T14:13:16Z")
I have had issues with the parallel = TRUE flag. No issues when parallele = FALSE. But when I put it to TRUE it just keeps hanging, even though I have 20 cores available. Replying to “I have had issues with the paralle… --- ## [Model Modification Indices and p-Hacking](https://isgw-forum.colorado.edu/t/model-modification-indices-and-p-hacking/877)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:12pm UTC](https://isgw-forum.colorado.edu/t/model-modification-indices-and-p-hacking/877 "2026-06-10T14:12:44Z")
Do you usually use model misspecification indices? To improve your model? one of the key features of CFA/SEM Replying to “Do you usually use model misspecification indices?..”: It’s good to check, but it’s also impor… --- ## [Separate GWAS Subsamples in Genomic SEM](https://isgw-forum.colorado.edu/t/separate-gwas-subsamples-in-genomic-sem/876)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:12pm UTC](https://isgw-forum.colorado.edu/t/separate-gwas-subsamples-in-genomic-sem/876 "2026-06-10T14:12:02Z")
If a GWAS reports summary statistics for separate subsamples (e.g., 23andMe and UK Biobank), should we meta-analyze them before using them in Genomic SEM? Replying to “If a GWAS reports summary statistics for separate … --- ## [Sample Size Per SNP](https://isgw-forum.colorado.edu/t/sample-size-per-snp/875)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 2:10pm UTC](https://isgw-forum.colorado.edu/t/sample-size-per-snp/875 "2026-06-10T14:10:56Z")
Regarding sample size, it can vary by SNP. Do we use the biggest sample size reported in the GWAS (biggest sample size per SNP)? Replying to “Regarding sample size, it can vary by SNP. Do we u…”: You can provide GSEM… --- ## [Using LMM GWAS Summary Statistics](https://isgw-forum.colorado.edu/t/using-lmm-gwas-summary-statistics/870)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:45pm UTC](https://isgw-forum.colorado.edu/t/using-lmm-gwas-summary-statistics/870 "2026-06-10T13:45:06Z")
Is there an issue using sumstats from GWAS using linear mixed models or am I getting confused with something else? Replying to “Is there an issue using sumstats from GWAS using l…”: No issues, as long as you appropri… --- ## [Practical Error Messages and Warnings](https://isgw-forum.colorado.edu/t/practical-error-messages-and-warnings/869)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:44pm UTC](https://isgw-forum.colorado.edu/t/practical-error-messages-and-warnings/869 "2026-06-10T13:44:19Z")
what does this error mean “Warning message: In FUN(X\[\[i\]\], …) : not all columns named in ‘colClasses’ exist” and why does it occur during the practical? Replying to "what does this error mean “Warning message: In FUN…… --- ## [Sumstats() Settings and Effect-Size Conversion](https://isgw-forum.colorado.edu/t/sumstats-settings-and-effect-size-conversion/868)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:43pm UTC](https://isgw-forum.colorado.edu/t/sumstats-settings-and-effect-size-conversion/868 "2026-06-10T13:43:18Z")
Are the latent variable “effects” (the est column in latent trait sumstats) always converted to continuous beta effects after GenomicSEM after using uswerGWAS () ? Replying to “Are the latent variable “effects” (the es… --- ## [Covariance Fixed to 1](https://isgw-forum.colorado.edu/t/covariance-fixed-to-1/867)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:41pm UTC](https://isgw-forum.colorado.edu/t/covariance-fixed-to-1/867 "2026-06-10T13:41:38Z")
When you fix a covariance to 1, does this mean in layman’s terms that the two variants perfectly covary? Replying to “When you fix a covariance to 1, does this mean in …”: Yep! Replying to “When you fix a covarianc… --- ## [HDL vs LDSC for Smaller Samples](https://isgw-forum.colorado.edu/t/hdl-vs-ldsc-for-smaller-samples/866)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:37pm UTC](https://isgw-forum.colorado.edu/t/hdl-vs-ldsc-for-smaller-samples/866 "2026-06-10T13:37:58Z")
Can we replace LDSC with something like HDL to give more accurate results for smaller datasets or is GSEM from smaller cohorts (or Z\<4) unreliable too? Replying to “Can we replace LDSC with something like HDL to giv…”: … --- ## [Preregistration](https://isgw-forum.colorado.edu/t/preregistration/865)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:35pm UTC](https://isgw-forum.colorado.edu/t/preregistration/865 "2026-06-10T13:35:08Z")
Register hypothesis where? Hi where do I pre-register my hypothesis? Replying to “Register hypothesis where?”: OSF Preregistration is one option: OSF They have pre-existing templates that you can fill out on the hy… --- ## [Drug Discovery Using Genomic SEM](https://isgw-forum.colorado.edu/t/drug-discovery-using-genomic-sem/864)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:32pm UTC](https://isgw-forum.colorado.edu/t/drug-discovery-using-genomic-sem/864 "2026-06-10T13:32:26Z")
Can we use GSEM for drug discovery as well? Replying to “Can we use GSEM for drug discovery as well?”: If you do the GWAS step after the initial modelling then you can use those results for many different drug discov… --- ## [Twin Samples and PRS](https://isgw-forum.colorado.edu/t/twin-samples-and-prs/863)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:31pm UTC](https://isgw-forum.colorado.edu/t/twin-samples-and-prs/863 "2026-06-10T13:31:46Z")
When working with twin simples and PGS, what is the preferred approach for accounting for relatedness? Is it sufficient to model family structure using a random effect (e.g., 1 | FAMID), or is it preferable to account fo… --- ## [HLA Regions and PRS](https://isgw-forum.colorado.edu/t/hla-regions-and-prs/862)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:30pm UTC](https://isgw-forum.colorado.edu/t/hla-regions-and-prs/862 "2026-06-10T13:30:15Z")
How are the genomic regions related to the HLA region best handled, in terms of their complex LD structure? Often the region is simply excluded, but what if the HLA regions are biologically relevant for the phenotype (e.… --- ## [Family Clustering but Weak Genetic Correlations](https://isgw-forum.colorado.edu/t/family-clustering-but-weak-genetic-correlations/861)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:29pm UTC](https://isgw-forum.colorado.edu/t/family-clustering-but-weak-genetic-correlations/861 "2026-06-10T13:29:13Z")
If I have a set of traits that, based on standard epidemiological studies, are known to cluster in families (for example lymphomas and autoimmune diseases), but the genetic correlation matrix shows limited genetic correl… --- ## [SEM Across Very Different Traits](https://isgw-forum.colorado.edu/t/sem-across-very-different-traits/860)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:27pm UTC](https://isgw-forum.colorado.edu/t/sem-across-very-different-traits/860 "2026-06-10T13:27:52Z")
is it possible to run SEM on traits totaly different like Cancer and Psychiatric disorders? Replying to “is it possible to run SEM on traits totaly differe…”: yes Replying to “is it possible to run SEM on traits to… --- ## [Genetic vs Phenotypic Correlation](https://isgw-forum.colorado.edu/t/genetic-vs-phenotypic-correlation/859)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:27pm UTC](https://isgw-forum.colorado.edu/t/genetic-vs-phenotypic-correlation/859 "2026-06-10T13:27:01Z")
Sorry, how exactly does genotypic correlation differs from phenotypic correlation? Replying to “Sorry, how exactly does genotypic correlation diff…”: The concepts are interpreted the same way, but for rG we are only … --- ## [Genomic SEM with Complete Sample Overlap](https://isgw-forum.colorado.edu/t/genomic-sem-with-complete-sample-overlap/858)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:25pm UTC](https://isgw-forum.colorado.edu/t/genomic-sem-with-complete-sample-overlap/858 "2026-06-10T13:25:17Z")
If I generate summary statistics for a set of traits from my own individual-level genetic data, can gemonicSME applied to this set of traits with almost 100% sample overlap? Replying to “If I generate summary statistic… --- ## [What Is Multivariate GWAS?](https://isgw-forum.colorado.edu/t/what-is-multivariate-gwas/857)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:23pm UTC](https://isgw-forum.colorado.edu/t/what-is-multivariate-gwas/857 "2026-06-10T13:23:41Z")
Is Multivariate GWAS a GWAS with multiple phenotypes at once? What is the exact definition? In simple terms, what is the output/result of Multivariate GWAS? Variants associated with several traits at once…? Replying t… --- ## [GWAS-by-Subtraction, Cog, and NonCog](https://isgw-forum.colorado.edu/t/gwas-by-subtraction-cog-and-noncog/856)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:23pm UTC](https://isgw-forum.colorado.edu/t/gwas-by-subtraction-cog-and-noncog/856 "2026-06-10T13:23:01Z")
In the GWAS by subtraction lecture, the COG latent factor was described ‘causing’ the CP observed variable. Given that the CP observed variable is not a direct measure of cognitive performance but rather the summary stat… --- ## [LDSC, Shared Genetics, and LD Scores](https://isgw-forum.colorado.edu/t/ldsc-shared-genetics-and-ld-scores/855)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:21pm UTC](https://isgw-forum.colorado.edu/t/ldsc-shared-genetics-and-ld-scores/855 "2026-06-10T13:21:02Z")
I am not sure what the SNP LD contributes to interpretation of shared genetics across traits; If a SNP is highly significant in sumstats for both trait 1 and trait 2, would LD score regression “devalue” this SNP, in term… --- ## [Mixed Binary and Continuous Traits in Genomic SEM](https://isgw-forum.colorado.edu/t/mixed-binary-and-continuous-traits-in-genomic-sem/854)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:19pm UTC](https://isgw-forum.colorado.edu/t/mixed-binary-and-continuous-traits-in-genomic-sem/854 "2026-06-10T13:19:17Z")
How to set arguments like se.logit, linprob, and OLS for running multivariate GWAS, when there are both continuous and binary variables? Replying to “How to set arguments like se.logit, linprob, and O…”: You would sp… --- ## [Sample Size Requirements for LDSC / Genomic SEM](https://isgw-forum.colorado.edu/t/sample-size-requirements-for-ldsc-genomic-sem/853)
**Author:** [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 1:18pm UTC](https://isgw-forum.colorado.edu/t/sample-size-requirements-for-ldsc-genomic-sem/853 "2026-06-10T13:18:00Z")
does sample size matter in LDsc regression. I mean can use GWAS with samples less than 1000 for LDsc? Yes, not advised for samples less than 5k. Replying to “does sample size matter in LDsc regression. I mean…”: you… [Previous page](https://isgw-forum.colorado.edu/c/isg-workshops-2026/28.md) [Next page](https://isgw-forum.colorado.edu/c/isg-workshops-2026/28.md?page=2)