diff options
| -rw-r--r-- | issues/phenotype-correlation-error.gmi | 16 |
1 files changed, 15 insertions, 1 deletions
diff --git a/issues/phenotype-correlation-error.gmi b/issues/phenotype-correlation-error.gmi index fa09f09..4d34dec 100644 --- a/issues/phenotype-correlation-error.gmi +++ b/issues/phenotype-correlation-error.gmi @@ -73,7 +73,11 @@ so far, triangulated the issue to possibly being the fact that the "target_datas ## Literature Correlation: ... -I also run into the following error when I run the mechanical-rob tests +Run literature correlation for +=> http://localhost:5033/show_trait?trait_id=1442370_at&dataset=HC_M2_0606_P this trait +against the "BXD Published Phenotype" database and observe the following exception: + +This also fails if you run it against the "BXD Genotypes" dataset. ``` ERROR:wqflask:http://localhost:5033/corr_compute ( 4:26AM UTC Oct 03, 2022) @@ -95,6 +99,16 @@ Traceback (most recent call last): 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". + +================== + +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 +that were run. + +Should these be present for the full correlations too? + ## Tags * assigned: alexm, fredm, zsloan * type: bug |