Error plotting heatmap

[tammyyyx]

Hi Dr. Weber,

Thanks for the awesome package! My data file is too big to use the built-in plotHeatmap function so I tried the plotDiffHeatMap from the Catalyst package, but got this error message "plotDiffHeatmap(out_DA$d_se, out_DA$res) Error in .check_sce(u$x, TRUE) : is(x, "SingleCellExperiment") is not TRUE"

The same error occurs when I apply the exact example codes from your diffcyt workflow on the exact sample dataset.

Could you help me with the problem? Is it because the package got updated? Thanks so much!

Regards,

Tammy

[sorjuela]

Hi @tammyyyx in the latest CATALYST (not sure what version you have, better to post your sessionInfo()), the first argument is the original SingleCellExperiment, the second argument is rowData(out_DA$res). You can follow the updated vignette here http://bioconductor.org/packages/release/bioc/vignettes/CATALYST/inst/doc/differential.html#plotdiffheatmap-heatmap-of-differential-testing-results

[lmweber]

Hi @tammyyyx , yes I believe we made some updates that may have affected this.

Are you using the latest versions of diffcyt and CATALYST from Bioconductor? (Bioconductor 3.11, diffcyt 1.8.8, CATALYST 1.12.2). If not, I recommend updating to the latest versions.

[tammyyyx]

Hi @lmweber,

I did update all packages but still got the same error message and hence the confusion. This happens with the example code and data from the diffcyt workflow.

Thanks for your time!

Tammy