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. :cursing_face:

[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.

[fishskywd]

Me too！when I use this GSVA in shihy，It bleak out.

[axelklenk]

Me too！when I use this GSVA in shihy，It bleak out.

Hi, thanks for using GSVA -- but this is not enough information to help you. As described above, there is a currently unsolved issue with the GSVA Shiny app when gene sets are provided in a list of character vectors.

If this is the issue you are experiencing, have you tried the workaround suggested above, i.e., convert your list into a GeneSetCollection, and does it solve the issue? If yes, that should help you to get things to work.

If not: you are experiencing a new and previously unknown issue and we'd like to have all information about it that you can give us, in particular you OS, version of R and GSVA, any output that is produced, and more information about your data set and gene sets and how you have been using the GSVA Shiny app -- with default options or particular choices that do or do not trigger the unexpected behavior? Please let us know, preferably in a new issue.

Cheers!