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mdozmorov / genome_runner

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Enrichment table to output adjusted and non-adjusted p-values #22

Closed mdozmorov closed 10 years ago

mdozmorov commented 10 years ago

Currently, enrichment analysis results are showing adjusted p-values, but the labels ("overrepresented"/"nonsignificant"/"underrepresented") pertain to the non-adjusted p-values. What may happen is:

wgEncodeUwDnaseHs27aHotspotsRep1 1 overrepresented wgEncodeCshlLongRnaSeqNhekCellPamContigs 1 nonsignificant

The first p-value was actually 0.03, but after correction became 1.

We need to output both adjusted and non-adjusted p-values for the table representation and the downloadable text version of the enrichment results.

mdozmorov commented 10 years ago

Also, the table on the web interface "Enrichment results" page currently shows "P-value" and "Direction" columns. However, the columns are messed up. It should be "Name" - the actual name of GF, "P-value" - the p-value, and "Direction" - currently missing, containing "over"/"under"/"nonsignificant" labels.

this seems to occur only when a "score" is set. If the score is "None", then 3 columns appear.

Bottom line: we need unified representation of the enrichment results with 4-columns: "Name" "P-value" "Adj. p-value" "Direction"

lkscara commented 10 years ago

Fixed in #20