Paul Pavlidis

Results 76 comments of Paul Pavlidis

Add "constitutively activating variant" as a subclass of "gain_of_function_variant"

Hi is anybody looking after this ontology?

Add "constitutively activating variant" as a subclass of "gain_of_function_variant"

No chance of getting any action on this? I see newer requests are being assigned, if this request is being denied please let me know, I appreciate it.

New term requests

Hi, is anybody looking after this ontology?

Could not order by factor: ExperimentalFactor Id=44646 Name=genotype Biomaterial count (16) does not equal the size of the reorganized biomaterial list (20). Check the experimental design for completeness/correctness

Needs more information. What experiment?

Updating a publication does not work reliably

I'm not sure anybody has managed to reproduce this.

Dataset show as "null" in the top diff. probes for subset analyses

I fixed this. #1070 was a duplicate.

Error while removing DEA

Still relevant? The error: ``` [Gemma - pool-280-thread-18 (2023-10-13 14:17:34,225)] ERROR ubic.gemma.persistence.retry.RetryLogger.close(50) | Retry failed after 2 attempts. NullPointerException: No ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis with ID 336360. java.lang.NullPointerException: No ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis with ID 336360....

Error while indexing in Hibernate Search

I thought we had migrated away from Hibernate search entirely, so is this still relevant?

quantitation type validation error

I'm seeing this for many other data sets as well like GSE228997, GSE228156 - maybe it is happening always, not sure

quantitation type validation error

We really need to eliminate the excessive false positives. This is for an RNA-seq experiment where we always have control over the scaling. If this is unavoidable, then disable all...