Paul Pavlidis
Paul Pavlidis
To address curation issue 362. By using the the `noLog2cpm` option for RNASeqDataAddCli should allow us to backfill counts and rpkm for old data sets in a minimally-invasive way. Needs...
This is useful for debugging. I only added one test. Relevant to https://github.com/PavlidisLab/GemmaCuration/issues/218 so ExpressionDataDoubleMatrixUtil is touched
As per #64 This should be added as a field to the API and probably displayed on the UI. Consider making more human-readable but not important.
For https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=33708 Clicking on the "view top genes" for some of the contrasts yields an error. (with some others it is okay) It is possible this is a duplicate of...
There is confusion about the semantics of "preferred" and there might be a basic error in how this works (probably my fault) The desired behaviour is for `preferred` to just...
It is extremely rare (
Nothing that the following are not used: ExperimentalDesign.replicateDescription, qualityControlDescription, normalizationDescription. ExperimentalDesign.types - this is only used in 9 experiments that were loaded from ArrayExpress, it isn't actually exposed or used...
The differential expression result files (such as those associated with DEAs here https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=20280) do not sufficiently document the meaning of the values. This is specifically an issue for "fold change"....
Assuming these are in the OWL file, they might be more useful for grouping chemicals than just the part-of/is-a relations. There are use cases for this: 1. For downstream applications...
On this page https://gemma.msl.ubc.ca/arrays/showAllArrayDesigns.html The dates shown for merged and subsumed platforms are often incorrect, at least for the sequence analysis. What is being shown is the date of update...