diff options
Diffstat (limited to 'issues')
| -rw-r--r-- | issues/phenotype-correlation-error.gmi | 39 |
1 files changed, 37 insertions, 2 deletions
diff --git a/issues/phenotype-correlation-error.gmi b/issues/phenotype-correlation-error.gmi index 8b37975..7bec588 100644 --- a/issues/phenotype-correlation-error.gmi +++ b/issues/phenotype-correlation-error.gmi @@ -71,8 +71,6 @@ KeyError: "'1422223_at' information is not found in the database." so far, triangulated the issue to possibly being the fact that the "target_dataset" value is not used => https://github.com/genenetwork/genenetwork2/blob/53aa084fd2c9c930ac791ee43affffb3f788547c/wqflask/wqflask/correlation/rust_correlation.py#L271-L289 in this function. -@zsloan and @alexm: any ideas? - ## Literature Correlation: Probeset Trait Against Publish/Genotype Dataset Run literature correlation for @@ -107,6 +105,9 @@ The code seems to imply that we should not run literature correlations against a ## Some Reflections +The `target_dataset` is not used in the +=> https://github.com/genenetwork/genenetwork2/blob/c38bee43c1256c3515bbd1d805745d8dfb8ce390/wqflask/wqflask/correlation/rust_correlation.py#L271-L289 tissue correlations which seems like an error to me (fredm). + 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. @@ -119,6 +120,40 @@ The failures above with the Publish/Genotype datasets implies one of two things: 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. +## Trial Against GN1 + +@zsloan @alexm: Running the failing tissue and literature correlations above with the same trait against the "BXD Published Phenotypes" and the "BXD Genotypes" on +=> http://gn1.genenetwork.org/ +I got the error +``` +Wrong correlation type + + Sorry! Error occurred while processing your request. + + The nature of the error generated is as follows: + + Correlation Type Error : + + It is not possible to compute the Tissue Correlation (Pearson's r) between your trait and data in this BXDGeno database. Please try again after selecting another type of correlation. +``` +for the tissue correlations and +``` +Wrong correlation type + + Sorry! Error occurred while processing your request. + + The nature of the error generated is as follows: + + Correlation Type Error : + + It is not possible to compute the SGO Literature Correlation between your trait and data in this BXDPublish database. Please try again after selecting another type of correlation. +``` +for the literature correlations. + +My initial hunch was correct. We should not be running the tissue and literature correlations in the way we were in the cases above. + +We now need to check for these combinations and display an error for the user, as is done in GN1 + ## Tags * assigned: alexm, fredm, zsloan * type: bug |