Frequently Asked Questions
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What does TW mean in the model names?
- We use TW to refer to the models trained with the original tissue expression. This makes sense in relation to the tissue specific expression models (TS*) we have derived using Orthogonal Tissue Decomposition See Details Here
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Are performance measures of prediction available?
- Yes, they can be found in the
extratable in each sqlite db.
- Yes, they can be found in the
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How many samples were used to train each model?
- This can be found in the
sample_infotable in each sqlite db.
- This can be found in the
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How do I query the prediction model db?
- Find example queries in here
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PrediXcan says my samples file has too few/too many rows.
- In order for the predicted expression file to be correct, the dosage files and samples file must correspond to the same individual. The columns for the dosage files are columns are snpid rsid position allele1 allele2 MAF id1 ..... idn and the samples file lists out the information for id1 ... idn row by row. As the id numbers are not included in the dosage file, it is critically important that the samples file has the same number of individuals in the same order as the dosages files. Otherwise later association tests will be invalid.