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Diffstat (limited to 'issues')
| -rw-r--r-- | issues/correlation_wrong_results.gmi | 27 |
1 files changed, 27 insertions, 0 deletions
diff --git a/issues/correlation_wrong_results.gmi b/issues/correlation_wrong_results.gmi new file mode 100644 index 0000000..c2685f3 --- /dev/null +++ b/issues/correlation_wrong_results.gmi @@ -0,0 +1,27 @@ +# Correlation results wrong for certain traits/datasets + +## Tags + +* assigned: alexm, zsloan, fredm +* priority: high +* status: ongoing + +* keywords: correlations + +## Description + +(Note that this uses the update to using GN! text files, but I don't think it's caused by that update) + +There are still a few remaining issues with correlations where the results are at least partially wrong. The ones I'm aware of are as follows: + +### Examples + +- http://gn2-zach.genenetwork.org/show_trait?trait_id=10710&dataset=BXDPublish (my branch linked because it's using the text file update) + +Correlate against "HQF Striatum Affy Mouse Exon 1.0ST Exon Level (Dec09) RMA" + +The results are a mix of correct and wrong ones. The top GN2 results have the same r/p values as their GN1 counterparts, but a number of top GN1 results are far lower on the list of GN2 results and have r values that are drastically lower. For example, 5200673 has the same r/p value in both GN1 and GN2, but 5169291 is the top GN1 result (with an r of -0.755), but in GN2 has an r of just 0.275 + +- https://genenetwork.org/show_trait?trait_id=24638&dataset=BXDPublish + +Correlate against BXD Published Phenotypes (the default). These results are almost all wrong, but in a way that is close to correct. I suspect the issue is that 0 values are being ommitted, since this seems to always occur when correlation with traits/datasets that have many sample values of 0. |