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| author | Frederick Muriuki Muriithi | 2022-10-04 11:56:55 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-10-04 11:56:55 +0300 |
| commit | fafce2504a5f716daa42c7c25e8dcdca2cec2c7a (patch) | |
| tree | df70423e9f39d232cf45fe8c97030f6dd51bf825 | |
| parent | 92b92785405f0cf7c6d88e1a5dbbe71e4d95632d (diff) | |
| download | gn-gemtext-fafce2504a5f716daa42c7c25e8dcdca2cec2c7a.tar.gz | |
Issues: (phenotype-correlation-error) Add more information
* Add notes on failures against the "BXD Genotypes" dataset
* Add some reflections
| -rw-r--r-- | issues/phenotype-correlation-error.gmi | 16 |
1 files changed, 13 insertions, 3 deletions
diff --git a/issues/phenotype-correlation-error.gmi b/issues/phenotype-correlation-error.gmi index 4d34dec..8b37975 100644 --- a/issues/phenotype-correlation-error.gmi +++ b/issues/phenotype-correlation-error.gmi @@ -41,12 +41,14 @@ KeyError: "'1' information is not found in the database." The error above was caused by processing the data for output way too early. This has been fixed. -## Tissue Correlation: Probeset Trait Against Publish Dataset +## Tissue Correlation: Probeset Trait Against Publish/Genotype Dataset Running "Tissue" correlations on => https://genenetwork.org/show_trait?trait_id=1442370_at&dataset=HC_M2_0606_P against the "BXD Published Phenotypes" database fails with the error: +This also fails if you run it against the "BXD Genotypes" dataset. + ``` Traceback (most recent call last): File "/usr/local/guix-profiles/gn-latest-20220820/lib/python3.9/site-packages/flask/app.py", line 1523, in full_dispatch_request @@ -71,7 +73,7 @@ so far, triangulated the issue to possibly being the fact that the "target_datas @zsloan and @alexm: any ideas? -## Literature Correlation: ... +## Literature Correlation: Probeset Trait Against Publish/Genotype Dataset Run literature correlation for => http://localhost:5033/show_trait?trait_id=1442370_at&dataset=HC_M2_0606_P this trait @@ -101,7 +103,9 @@ AttributeError: 'PhenotypeDataSet' object has no attribute 'retrieve_genes' The literature correlations computation calls the `retrieve_genes` method, that is only present in the `base.data_set.mrnaassaydataset.MrnaAssayDataSet` class, which handles traits of type "ProbeSet". -================== +The code seems to imply that we should not run literature correlations against any dataset that is not of type "ProbeSet". + +## Some Reflections In my (fredm) work on partial correlations, before doing the computations, => https://github.com/genenetwork/genenetwork3/blob/ff34aee0f39c2e91db243461d7d67405e7aea0e3/gn3/computations/partial_correlations.py#L704-L750 there were error checks @@ -109,6 +113,12 @@ that were run. Should these be present for the full correlations too? +The failures above with the Publish/Genotype datasets implies one of two things: +* The code is not general enough, or +* We need to handle the exceptions, and present the selection errors as appropriate. + +Better yet, we should probably not present invalid data to the user, i.e. do not present user with a dataset which would lead to errors if a correlation of a particular type is run against it with the given trait. + ## Tags * assigned: alexm, fredm, zsloan * type: bug |