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Welcome to the PrediXcan/MetaXcan user group. The goal of this group is to discuss issues arising from performing PrediXcan and MetaXcan. Your questions may have been solved before, make sure to search the mailing list or the predictdb.org's FAQ (https://predictdb.org/categories/faq/)

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Aug 28

PrediXcan Association Output Error

Hi, I ran PrediXcan using the MetaXcan package and I was able to successfully run the package using

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PrediXcan Association Output Error

Hi, I ran PrediXcan using the MetaXcan package and I was able to successfully run the package using

Aug 28

Mohamed Abdelrahman

Aug 7

Low Elastic Net R2 Prediction performance

Hello, We are having issues with low R2 (coefficient of determination) Predictions from the Elastic

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Low Elastic Net R2 Prediction performance

Hello, We are having issues with low R2 (coefficient of determination) Predictions from the Elastic

Aug 7

Hae Kyung Im, Festus2

Jun 20

Re: Request for Assistance with S-PrediXcan on UK Biobank WGS Data

Hi Faisal, I have seen a few issues with your code; In the command line argument –snp_column you are

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Re: Request for Assistance with S-PrediXcan on UK Biobank WGS Data

Hi Faisal, I have seen a few issues with your code; In the command line argument –snp_column you are

Jun 20

david davtian, Hae Kyung Im4

May 28

MultiXcan output not matching

Sure For example this is my MultiXcan output. And if I look into this first PNKP gene in

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MultiXcan output not matching

Sure For example this is my MultiXcan output. And if I look into this first PNKP gene in

May 28

Apr 27

Fwd: A question about MetaXcan

Dear Yanfa, I am forwarding this email to the PrediXcan mailing list where you can get help. Please

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Fwd: A question about MetaXcan

Dear Yanfa, I am forwarding this email to the PrediXcan mailing list where you can get help. Please

Apr 27

Apr 14

Request for Clarification on Generating Genotype.txt File for TWAS Analysis: To Train the Model

Hello, I am reaching out to seek clarification on generating the genotype.txt file required for

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Request for Clarification on Generating Genotype.txt File for TWAS Analysis: To Train the Model

Hello, I am reaching out to seek clarification on generating the genotype.txt file required for

Apr 14

Zurodher, … Sofía Salazar8

Apr 2

0% of model SNPs

Many thanks Sofia. Can I use something like this to instruct SPrediXcan.py to create a SNP ID in my

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0% of model SNPs

Many thanks Sofia. Can I use something like this to instruct SPrediXcan.py to create a SNP ID in my

Apr 2

Zurodher, Hae Kyung Im2

Mar 27

Repeated ARIC weights

Thank you, Zulema, for pointing that out. Sofia: could you please investigate? Sabrina: I believe you

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Repeated ARIC weights

Thank you, Zulema, for pointing that out. Sofia: could you please investigate? Sabrina: I believe you

Mar 27

Kalyani Kottilil, … Sofía Salazar9

Feb 25

0% of model SNPs used Predict.py

Hi Kalyani, I apologize for the late response. Looking at your file, the second example that you sent

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0% of model SNPs used Predict.py

Hi Kalyani, I apologize for the late response. Looking at your file, the second example that you sent

Feb 25

sudha...@gmail.com, Hae Kyung Im2

Feb 11

Package PEER doesn't exist anymore

You can use principal components of the gene expression matrix instead. It's been shown that PCs

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Package PEER doesn't exist anymore

You can use principal components of the gene expression matrix instead. It's been shown that PCs

Feb 11

Qianhui Xu, … Sofía Salazar7

Feb 5

Error running S-Multixcan

Hi, I have built and environment using the file you shared but I was still unable to replicate your

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Error running S-Multixcan

Hi, I have built and environment using the file you shared but I was still unable to replicate your

Feb 5

Olivia Zhang, Hae Kyung Im2

11/15/24

The example model: DGN-WB_0.5.db 's meaning

Hi Olivia These were based on whole blood. Battle 2013 in Genome research explains the expression

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The example model: DGN-WB_0.5.db 's meaning

Hi Olivia These were based on whole blood. Battle 2013 in Genome research explains the expression

11/15/24

Fotis Tsetsos, Hae Kyung Im3

11/3/24

Predictdb.org is down

Actually it's working now On Sun, Nov 3, 2024 at 11:48 AM Hae Kyung Im <hak...@gmail.com>

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Predictdb.org is down

Actually it's working now On Sun, Nov 3, 2024 at 11:48 AM Hae Kyung Im <hak...@gmail.com>

11/3/24

10/9/24

Integrating MetaXcan with eQTL Databases Built Using TensorQTL

Dear Community, Thank you for developing MetaXcan and setting up this Google Group. We have already

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Integrating MetaXcan with eQTL Databases Built Using TensorQTL

Dear Community, Thank you for developing MetaXcan and setting up this Google Group. We have already

10/9/24

9/24/24

Inquiry Regarding Column Definitions in GWAS Summary Imputation Output File

Dear Community, I hope this message finds you well. I am currently utilizing the

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Inquiry Regarding Column Definitions in GWAS Summary Imputation Output File

Dear Community, I hope this message finds you well. I am currently utilizing the

9/24/24

8/28/24

Re: PredictDB Data Repository

Thank you, Narges, for bringing this to my attention. It seems that zenodo made some changes to their

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Re: PredictDB Data Repository

Thank you, Narges, for bringing this to my attention. It seems that zenodo made some changes to their

8/28/24

5/13/24

Fwd: Questions related to PrediXcan

Hi, please see below for responses Haky Using GTEx data as the reference transcriptome, you trained

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Fwd: Questions related to PrediXcan

Hi, please see below for responses Haky Using GTEx data as the reference transcriptome, you trained

5/13/24

Maciel Rodriguez, Hae Kyung Im2

5/13/24

INFO - Gene ENSG... has covariance close to singular

That's a red flag for numerical issues. My guess is that you don't have enough SNPs in your

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INFO - Gene ENSG... has covariance close to singular

That's a red flag for numerical issues. My guess is that you don't have enough SNPs in your

5/13/24

Maciel Rodriguez

5/9/24

Should rows with few n_snps_used be filtered out?

Hi! Thank you so much for this amazing tool! It is helping me a lot :) I wanted to know if I should

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Should rows with few n_snps_used be filtered out?

Hi! Thank you so much for this amazing tool! It is helping me a lot :) I wanted to know if I should

5/9/24

Maciel Rodriguez

5/6/24

Extremely low P-values or P-values equal to zero and very high and low effect sizes

Hi, first of all, thank you so much for this wonderful tool! It's helping me a lot with my

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Extremely low P-values or P-values equal to zero and very high and low effect sizes

Hi, first of all, thank you so much for this wonderful tool! It's helping me a lot with my

5/6/24

jfe...@gmail.com

5/6/24

mashr model weights

Hi all, I am trying to run Predixcan using mashr models created from my own data. I am using the

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mashr model weights

Hi all, I am trying to run Predixcan using mashr models created from my own data. I am using the

5/6/24

4/24/24

[Minor allele frequency of SNP in gene prediction model based on GTEx data in PrediXcan, elastic net model]

Hello, wonderful MetaXcan team ! Thank you for your resources related with the gene expression

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[Minor allele frequency of SNP in gene prediction model based on GTEx data in PrediXcan, elastic net model]

Hello, wonderful MetaXcan team ! Thank you for your resources related with the gene expression

4/24/24

Maciel Rodriguez

4/16/24

P-Values or Adjusted P-Values

Hi! First of all, I wanted to thank you for this wonderful tool! It's really helping me a lot

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P-Values or Adjusted P-Values

Hi! First of all, I wanted to thank you for this wonderful tool! It's really helping me a lot

4/16/24

Dorothy Chen, Hae Kyung Im4

4/16/24

Mashr models: Sample Size and Expression Prediction Models

Thank you! I just wanted to check and see if there have been any updates since the last email. On

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Mashr models: Sample Size and Expression Prediction Models

Thank you! I just wanted to check and see if there have been any updates since the last email. On

4/16/24

xinyu liang, Hae Kyung Im2

3/17/24

How to convert the result predicted by PrediXcan to the real TPM value

You should be getting a range of correlations (squared shown in the figure), so there is something

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How to convert the result predicted by PrediXcan to the real TPM value

You should be getting a range of correlations (squared shown in the figure), so there is something

3/17/24

Anmol Singh, … Festus4

2/12/24

0% of model SNPs used Error in S-Predixcan

Great, that worked. Thank you!! On Monday, February 12, 2024 at 10:25:46 AM UTC-6 Festus wrote: You

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0% of model SNPs used Error in S-Predixcan

Great, that worked. Thank you!! On Monday, February 12, 2024 at 10:25:46 AM UTC-6 Festus wrote: You

2/12/24

2/6/24

Inquiry related to using S-Predixcan for doing association study.

Hello All, I am interested in using PrediXcan to do association study. I see that we can use S-

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Inquiry related to using S-Predixcan for doing association study.

Hello All, I am interested in using PrediXcan to do association study. I see that we can use S-

2/6/24

1/13/24

About generate imputation reference data

I apologize for frequent disruptions. However, I would like to verify if using my own metadata would

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About generate imputation reference data

I apologize for frequent disruptions. However, I would like to verify if using my own metadata would

1/13/24

jfe...@gmail.com

12/28/23

get GTEx variant metadata in parquet format

Hi all, I am trying to get the reference metadata using GTEx data (we have access through dbGAP),

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get GTEx variant metadata in parquet format

Hi all, I am trying to get the reference metadata using GTEx data (we have access through dbGAP),

12/28/23

Juan Fernandez-Tajes

12/13/23

Code for generate mashr models with my own data

Hi, I was wondering if any on this list have any code or pseudo code for generating mashr models from

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Code for generate mashr models with my own data

Hi, I was wondering if any on this list have any code or pseudo code for generating mashr models from

12/13/23

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