GSEA Desktop v4.2.x

GSEA Desktop v4.2.3 (Mar 2022)#

GSEA v4.2.3 is a security release, removing Log4J entirely from the code base. All users are encouraged to update! This also fixes an additional bug in the weighted_p1.5 scoring mode. If you have used this mode in the past, we recommend re-running your analysis with GSEA 4.2.3 to evaluate the possible differences. Minimum dataset size warnings have been added as well, to note that GSEA should be run with data from all expressed genes rather than a reduced subset or "Top DEGs" list.

GSEA Desktop v4.2.2 (Jan 2022)#

GSEA v4.2.2 is a security release, updating to Log4J 2.17.1. All users are encouraged to update!

GSEA Desktop v4.2.1 (Dec 2021)#

GSEA v4.2.1 is a security release, updating to Log4J 2.17.0. All users are encouraged to update!

There is one minor bug fix to the TXT parser to fix an error when no Description column is present. There are no other changes.

GSEA Desktop v4.2.0 (Dec 2021)#

The GSEA v4.2.0 release includes a number of improvements and bug fixes, including:

There are also updates for better handling of missing values in the input datasets in the file parsers and computations. GSEA ignores missing values in general but there were certain situations where this was not the case. These happened primarily around missing tab fields and explicit NA or NaN input values, but there were also improvements to the handling of missing values overall.

Likewise, there are also updates to provide warnings about explicit infinite values in the input dataset. Such values can cause unexpected results during computation or plotting and are not recommended. Infinite values in the input will, however, be handled and used as-is in the metric computations.

Infinite values coming out of the metric computations will be adjusted to a small value when using the various "weighted" scoring modes, to avoid interfering with the rest of the enrichment results and any subsequent reporting. This has the effect of de-emphasizing that particular gene in any scoring.

This adjustment has historically been applied to the "weighted" scoring modes but was not previously documented. For the "weighted" mode, the value is adjusted to 0.01. For the "weighted_p1.5" and "weighted_p2" modes it is adjusted to 0.000001. The adjustment is not applied to the Classic K-S scoring mode since the expression values are not directly used with this mode.

A similar adjustment is also made to infinite values during plotting to avoid errors from the charting library being unable to render such values.

Warnings are also provided for Infinite or NaN values coming out of metric computations (resulting from division-by-zero or taking the root of a negative value, for example).

The vast majority of datasets should be unaffected by these changes as such values should be relatively rare. If you have run analyses on datasets with missing, NA, NaN, or Infinite values and are concerned about changes to the results, we recommend re-running the analysis with GSEA 4.2.0 to evaluate the possible differences.

Beyond that, there are a number of miscellaneous improvements and bug fixes. Chief among these are: