Error when using Data Input From Workspace in Shiny app

[axelklenk]

When testing the Shiny app, Data Input From File worked as before, whereas Data Input From Workspace resulted in the error message below (this used to work fine):

Error in validObject(.Object): invalid class "gsvaParam" object: invalid object for slot "geneSets" in class "gsvaParam": got class "reactive.cache", should be or extend class "GsvaGeneSets"

Apparently the error message comes from validation of the parameter object, where something called a reactive.cacheis found when one of our classes is expected. 🤬

[axelklenk]

Sorry, GitHub, we're not finished yet: there's at least two more bugs remaining in the Shiny app waiting to be fixed.

[terbanacle]

Hi, I am also running the Shiny app and I got the following error message when using data on the Workspace. This happens on both GSVA v2.0.1 and v2.0.4.

Error in validObject(.Object): invalid class “gsvaParam” object: invalid object for slot "geneSets" in class "gsvaParam": got class "gsvaParam", should be or extend class "GsvaGeneSets"

[axelklenk]

Hi,

an update on this issue: while I have not yet been able to find its cause and fix it, it will only occur

1. when using GSVAvia the Shiny app, and
2. supplying the gene sets as a list of character vectors,
   i.e., as a workaround you can either

• (in your workspace) convert your gene set list into a GSEABase::GeneSetCollection by using GSVA function geneIdsToGeneSetCollection() and (from the Shiny app) select the resulting object from the workspace, or
• read gene sets from a GMT file as the internal read function will always return a GeneSetCollection object.

Please make sure to use GSVA version 2.0.5 (available as of today) that fixes another bug in the Shiny app 😅 which had caused all invocations of the default method GSVA to fail.